Anti-HER2 glycoantibodies and uses thereof

Abstract

The present disclosure relates to a novel class of anti-HER2 monoclonal antibodies comprising a homogeneous population of anti-HER2 IgG molecules having the same N-glycan on each of Fc. The antibodies of the invention can be produced from anti-HER2 monoclonal antibodies by Fc glycoengineering. Importantly, the antibodies of the invention have improved therapeutic values with increased ADCC activity and increased Fc receptor binding affinity compared to the corresponding monoclonal antibodies that have not been glycoengineered.

Claims

1. A method of treating a HER2-expressing breast tumor in a patient in need thereof, the method comprising administering to the patient an effective amount of a pharmaceutical formulation comprising an anti-HER2 monoclonal antibody or antigen binding fragment thereof, comprising a homogeneous population of anti-HER2 IgG molecules, wherein the anti-HER2 monoclonal antibody or antigen binding fragment thereof has been glycoengineered to have the same N-glycan attached to the Asn-297 on the Fc region of each anti-HER2 IgG molecule, wherein the N-glycan is selected from the group consisting of Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-3)GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia(2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia(2-6)GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-3)GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-6)GalGlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Sia(2-3)GalGlcNAc.sub.3Man.sub.3GlcNAc.sub.2, Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2 and Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GalGlcNAc.sub.3Man.sub.3GlcNAc.sub.2, GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GlcNAcMan.sub.3GlcNAc.sub.2 and Man.sub.3GlcNAc.sub.2, and wherein the glycoengineered anti-HER2 antibody or fragment thereof has increased ADCC activity as compared to Trastuzumab or stronger FcRIIIA binding activity as compared to Trastuzumab or a combination of increased ADCC activity and stronger FcRIIIA binding activity as compared to Trastuzumab.

2. The method of claim 1, wherein said HER2-overexpressing tumor is breast cancer.

3. The method of claim 1, further comprising administering to the patient a therapeutic agent.

4. The method of claim 1, wherein the N-glycan is selected from the group consisting of Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, and Man.sub.3GlcNAc.sub.2.

5. The method of claim 1, wherein the N-glycan is selected from the group consisting of Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Sia(2-6)GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GalGlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GalGlcNAcMan.sub.3GlcNAc.sub.2, GlcNAc.sub.3Man.sub.3GlcNAc.sub.2, GlcNAc.sub.2Man.sub.3GlcNAc.sub.2, GlcNAcMan.sub.3GlcNAc.sub.2 and Man.sub.3GlcNAc.sub.2.

6. The method of claim 1, wherein the N-glycan is Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc.sub.2.

7. The method of claim 1, wherein the antibody is Trastuzumab or Pertuzumab.

8. The method of claim 1, wherein the antibody comprises a heavy chain amino acid sequence as set forth in SEQ ID NO. 1 and a light chain amino acid sequence as set forth in SEQ ID NO. 2.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 shows a schematic representation of Fc glycoengineering of monoclonal antibodies. Route (A) shows the methods known in the art that lead to a mixture of fucosylated and nonfucosylated antibodies. Route (B) shows the method of the present invention that leads to a homogeneous glycoantibodies.

(2) FIG. 2 shows SDS-PAGE analyses of anti-HER2 GAbs 102, 102, 104, 105, 106, 107, 108, 110 and 111.

(3) FIG. 3 shows the intact molecular weight of anti-HER2 GAb101 by ESI/MS.

(4) FIG. 4 shows the intact molecular weight of anti-HER2 GAb104 by ESI/MS.

(5) FIG. 5 shows the MS spectrum of the cleavaged glycopeptide TKPREEQYNSTYR (SEQ ID NO: 3) after trypsin digestion of anti-HER2 GAbs 101. FIG. 5 discloses EEQYNSTYR as SEQ ID NO: 4.

(6) FIG. 6 shows MS spectrum of the cleavaged glycopeptide TKPREEQYNSTYR (SEQ ID NO: 3) after trypsin digestion of anti-HER2 GAbs 104. FIG. 6 discloses EEQYNSTYR as SEQ ID NO: 4.

(7) FIG. 7 shows ADCC activities of anti-HER2 GAbs 101, 102, 104, 106, 107, 108, and Trastuzumab. Rituximab was used as a negative control.

(8) FIG. 8 shows exemplary N-glycans of anti-HER2 glycoantibodies. Embodiments of the present disclosure may include or exclude any of the N-glycans listed herein.

(9) FIG. 9 shows exemplary N-glycans of anti-HER2 glycoantibodies. Embodiments of the present disclosure may include or exclude any of the N-glycans listed herein.

(10) FIG. 10 shows exemplary N-glycans of anti-HER2 glycoantibodies. Embodiments of the present disclosure may include or exclude any of the N-glycans listed herein.

(11) FIG. 11 shows exemplary N-glycans of anti-HER2 glycoantibodies. Embodiments of the present disclosure may include or exclude any of the N-glycans listed herein.

(12) FIG. 12 shows the building blocks of glycosylation methods used as described herein.

(13) FIG. 13 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(14) FIG. 14 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(15) FIG. 15 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(16) FIG. 16 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(17) FIG. 17 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(18) FIG. 18 shows schemes for synthesizing exemplary asymmetric N-glycans of this disclosure.

(19) FIG. 19 shows a table listing N-glycan profiling of exemplary anti-HER2 glycosylated antibodies (GAbs) of this disclosure.

(20) FIG. 20 shows the results of ELISA binding for exemplary N-glycans of this disclosure.

DETAILED DESCRIPTION OF THE INVENTION

(21) Accordingly, a need remains for improving monoclonal antibody therapy with improved anti-HER2 antibodies. A few specific glycoforms in the heterogeneous mixtures of glycosylation patterns are known to confer desired biological functions. Thus, it is of great interest to generate therapeutic antibodies contain a well-defined glycan structure and sequence as desired glycoforms for therapeutic purposes.

(22) The present disclosure relates to the development of a novel class of monoclonal antibodies, named glycoantibodies. The term glycoantibodies was coined by the inventor, Dr. Chi-Huey Wong, to refer to a homogeneous population of monoclonal antibodies (preferably, therapeutic monoclonal antibodies) having a single, uniform glycoform on Fc. The individual glycoantibodies comprising the homogeneous population are identical, bind to the same epitope, and contain the same Fc glycan with a well-defined glycan structure and sequence.

(23) The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Antibodies: A Laboratory Manual, by Harlow and Lane s (Cold Spring Harbor Laboratory Press, 1988); and Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986).

Definitions

(24) As used herein, the term glycan refers to a polysaccharide, oligosaccharide or monosaccharide. Glycans can be monomers or polymers of sugar residues and can be linear or branched. A glycan may include natural sugar residues (e.g., glucose, N-acetylglucosamine, N-acetyl neuraminic acid, galactose, mannose, fucose, hexose, arabinose, ribose, xylose, etc.) and/or modified sugars (e.g., 2-fluororibose, 2-deoxyribose, phosphomannose, 6 sulfo N-acetylglucosamine, etc). Glycan is also used herein to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, glycopeptide, glycoproteome, peptidoglycan, lipopolysaccharide or a proteoglycan. Glycans usually consist solely of O-glycosidic linkages between monosaccharides. For example, cellulose is a glycan (or more specifically a glucan) composed of -1,4-linked D-glucose, and chitin is a glycan composed of -1,4-linked N-acetyl-D-glucosamine. Glycans can be homo or heteropolymers of monosaccharide residues, and can be linear or branched. Glycans can be found attached to proteins as in glycoproteins and proteoglycans. They are generally found on the exterior surface of cells. 0- and N-linked glycans are very common in eukaryotes but may also be found, although less commonly, in prokaryotes. N-Linked glycans are found attached to the R-group nitrogen (N) of asparagine in the sequon. The sequon is a Asn-X-Ser or Asn-X-Thr sequence, where X is any amino acid except praline.

(25) As used herein, the terms fucose, core fucose and core fucose residue are used interchangeably and refer to a fucose in a 1,6-position linked to the N-acetylglucosamine.

(26) As used herein, the term fucosylated refers to the presence of a core fucose in the N-glycan of Fc, whereas the term defucosylated refers to the absence of a core fucose in the N-glycan of Fc.

(27) As used herein, the terms N-glycan, N-linked glycan, N-linked glycosylation, Fc glycan and Fc glycosylation are used interchangeably and refer to an N-linked oligosaccharide attached by an N-acetylglucosamine (GlcNAc) linked to the amide nitrogen of an asparagine residue in a Fc-containing polypeptide. The term Fc-containing polypeptide refers to a polypeptide, such as an antibody, which comprises an Fc region.

(28) As used herein, the term glycosylation pattern and glycosylation profile are used interchangeably and refer to the characteristic fingerprint of the N-glycan species that have been released from a glycoprotein or antibody, either enzymatically or chemically, and then analyzed for their carbohydrate structure, for example, using LC-HPLC, or MALDI-TOF MS, and the like. See, for example, the review in Current Analytical Chemistry, Vol. 1, No. 1 (2005), pp. 28-57; herein incorporated by reference in its entirety.

(29) As used herein, the term glycoengineered Fc when used herein refers to N-glycan on the Fc region has been altered or engineered either enzymatically or chemically. The term Fc glycoengineering as used herein refers to the enzymatic or chemical process used to make the glycoengineered Fc. Exemplary methods of engineering are described in, for example, Wong et al U.S. Ser. No. 12/959,351, the contents of which is hereby incorporated by reference.

(30) The term effector function as used herein refers to a biochemical event that results from the interaction of an antibody Fc region with an Fc receptor or ligand. Exemplary effector functions include complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g. B cell receptor; BCR), etc. Such effector functions can be assessed using various assays known in the art.

(31) As used herein, the term Antibody-dependent cell-mediated cytotoxicity or ADCC refers to a form of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs) present on certain cytotoxic cells (e.g. Natural Killer (NK) cells, neutrophils, and macrophages) enable these cytotoxic effector cells to bind specifically to an antigen-bearing target cell and subsequently kill the target cell with cytotoxins. The antibodies arm the cytotoxic cells and are absolutely required for such killing. The primary cells for mediating ADCC, NK cells, express FcRIII only, whereas monocytes express FcRI, FcRII and FcRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). To assess ADCC activity of a molecule of interest, an in vitro ADCC assay, such as that described in U.S. Pat. Nos. 5,500,362 or 5,821,337 may be performed. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in an animal model such as that disclosed in Clynes et al. PNAS (USA) 95:652-656 (1998).

(32) The term Complement dependent cytotoxicity or CDC as used herein refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (C1q) to antibodies (of the appropriate subclass) which are bound to their cognate antigen. To assess complement activation, a CDC assay, e.g. as described in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), may be performed.

(33) An antibody that induces apoptosis is one which induces programmed cell death as determined by binding of annexin V, fragmentation of DNA, cell shrinkage, dilation of endoplasmic reticulum, cell fragmentation, and/or formation of membrane vesicles (called apoptotic bodies). Preferably the cell is an infected cell. Various methods are available for evaluating the cellular events associated with apoptosis. For example, phosphatidyl serine (PS) translocation can be measured by annexin binding; DNA fragmentation can be evaluated through DNA laddering; and nuclear/chromatin condensation along with DNA fragmentation can be evaluated by any increase in hypodiploid cells. Preferably, the antibody that induces apoptosis is one that results in about 2 to 50 fold, preferably about 5 to 50 fold, and most preferably about 10 to 50 fold, induction of annexin binding relative to untreated cell in an annexin binding assay.

(34) Chimeric antibodies (immunoglobulins) have a portion of the heavy and/or light chain identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al., Proc. Natl. Acad Sci. USA 81:6851-6855 (1984)). Humanized antibody as used herein is a subset of chimeric antibodies.

(35) Humanized forms of non-human (e.g., murine) antibodies are chimeric antibodies which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient or acceptor antibody) in which hypervariable region residues of the recipient are replaced by hypervariable region residues from a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity. In some instances, Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues which are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance such as binding affinity. Generally, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin sequence although the FR regions may include one or more amino acid substitutions that improve binding affinity. The number of these amino acid substitutions in the FR is typically no more than 6 in the H chain, and in the L chain, no more than 3. The humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321:522-525 (1986); Reichmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992).

(36) Treating or treatment or alleviation refers to both therapeutic treatment and prophylactic or preventative measures; wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented. A subject or mammal is successfully treated for an infection if after receiving a therapeutic amount of an antibody according to the methods of the present invention, the patient shows observable and/or measurable reduction in or absence of one or more of the following: reduction in the number of infected cells or absence of the infected cells; reduction in the percent of total cells that are infected; and/or relief to some extent, one or more of the symptoms associated with the specific infection; reduced morbidity and mortality, and improvement in quality of life issues. The above parameters for assessing successful treatment and improvement in the disease are readily measurable by routine procedures familiar to a physician.

(37) Administration in combination with one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

(38) Carriers as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN polyethylene glycol (PEG), and PLURONICS

(39) The term glycoantibodies was coined by the inventor, Dr. Chi-Huey Wong, to refer to a homogeneous population of monoclonal antibodies (preferably, therapeutic monoclonal antibodies) having a single, uniformed glycoform bound to the Fc region. The individual glycoantibodies comprising the essentially homogeneous population are identical, bind to the same epitope, and contain the same Fc glycan with a well-defined glycan structure and sequence.

(40) The terms homogeneous, uniform, uniformly and homogeneity in the context of a glycosylation profile of Fc region are used interchangeably and are intended to mean a single glycosylation pattern represented by one desired N-glycan species, with little or no trace amount of precursor N-glycan. In certain embodiments, the trace amount of the precursor N-glycan is less than about 2%.

(41) Essentially pure protein means a composition comprising at least about 90% by weight of the protein, based on total weight of the composition, including, for example, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% by weight.

(42) Essentially homogeneous protein means a composition comprising at least about 98% by weight of protein, including for example, at least about 98.5%, at least about 99% based on total weight of the composition. In certain embodiments, the protein is an antibody, structural variants, and/or antigen binding fragment thereof.

(43) As used herein, the terms IgG, IgG molecule, monoclonal antibody, immunoglobulin, and immunoglobulin molecule are used interchangeably. As used herein, molecule can also include antigen binding fragments.

(44) As used herein, the term Fc receptor or FcR describes a receptor that binds to the Fc region of an antibody. The preferred FcR is a native sequence human FcR. Moreover, a preferred FcR is one which binds an IgG antibody (a gamma receptor) and includes receptors of the FcRI (CD64), FcRII (CD32), and FcRIII (CD16) subclasses, including allelic variants and alternatively spliced forms of these receptors. FcRII receptors include FcRIIA (an activating receptor) and FcRIIB (an inhibiting receptor), which have similar amino acid sequences that differ primarily in the cytoplasmic domains thereof. Activating receptor FcRIIA contains an immunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmic domain. Inhibiting receptor FcRIIB contains an immunoreceptor tyrosine-based inhibition motif (TIM) in its cytoplasmic domain. (see review M. in Daeron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med. 126:330-41 (1995). Other FcRs, including those to be identified in the future, are encompassed by the term FcR herein. The term also includes the neonatal receptor, FcRn, which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)).

(45) As used herein, the term antigen is defined as any substance capable of eliciting an immune response. As used herein, the term antigen specific refers to a property of a cell population such that supply of a particular antigen, or a fragment of the antigen, results in specific cell proliferation.

(46) As used herein, the term immunogenicity refers to the ability of an immunogen, antigen, or vaccine to stimulate an immune response.

(47) As used herein, the term epitope is defined as the parts of an antigen molecule which contact the antigen binding site of an antibody or a T cell receptor.

(48) As used herein, the term specifically binding, refers to the interaction between binding pairs (e.g., an antibody and an antigen). In various instances, specifically binding can be embodied by an affinity constant of about 10-6 moles/liter, about 10-7 moles/liter, or about 10-8 moles/liter, or less.

(49) An isolated antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with research, diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.

(50) The phrase substantially similar, substantially the same, equivalent, or substantially equivalent, as used herein, denotes a sufficiently high degree of similarity between two numeric values (for example, one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values, anti-viral effects, etc.). The difference between said two values is, for example, less than about 50%, less than about 40%, less than about 30%, less than about 20%, and/or less than about 10% as a function of the value for the reference/comparator molecule.

(51) The phrase substantially reduced, or substantially different, as used herein, denotes a sufficiently high degree of difference between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values is, for example, greater than about 10%, greater than about 20%, greater than about 30%, greater than about 40%, and/or greater than about 50% as a function of the value for the reference/comparator molecule.

(52) Binding affinity generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, binding affinity refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd). Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention. Specific illustrative embodiments are described in the following.

(53) The variable region or variable domain of an antibody refers to the amino-terminal domains of heavy or light chain of the antibody. These domains are generally the most variable parts of an antibody and contain the antigen-binding sites.

(54) The term variable refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR). The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a beta-sheet configuration, connected by three CDRs, which form loops connecting and in some cases forming part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, Md. (1991)). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.

(55) Papain digestion of antibodies produces two identical antigen-binding fragments, called Fab fragments, each with a single antigen-binding site, and a residual Fc fragment, whose name reflects its ability to crystallize readily. Pepsin treatment yields an F(ab)2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.

(56) Fv is the minimum antibody fragment which contains a complete antigen-recognition and -binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. In a single-chain Fv species, one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a dimeric structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.

(57) The Fab fragment also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. Fab fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region. Fab-SH is the designation herein for Fab in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab)2 antibody fragments originally were produced as pairs of Fab fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.

(58) The light chains of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa () and lambda (), based on the amino acid sequences of their constant domains.

(59) Depending on the amino acid sequences of the constant domains of their heavy chains, antibodies (immunoglobulins) can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called , , , , and , respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known and described generally in, for example, Abbas et al. Cellular and Mol. Immunology, 4th ed. (2000). An antibody may be part of a larger fusion molecule, formed by covalent or non-covalent association of the antibody with one or more other proteins or peptides.

(60) The terms full length antibody, intact antibody and whole antibody are used herein interchangeably, to refer to an antibody in its substantially intact form, not antibody fragments as defined below. The terms particularly refer to an antibody with heavy chains that contain the Fc region.

(61) Antibody fragments comprise only a portion of an intact antibody, wherein the portion retains at least one, and as many as most or all, of the functions normally associated with that portion when present in an intact antibody. In one embodiment, an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen. In another embodiment, an antibody fragment, for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half life modulation, ADCC function and complement binding. In one embodiment, an antibody fragment is a monovalent antibody that has an in vivo half life substantially similar to an intact antibody. For example, such an antibody fragment may comprise an antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment.

(62) The term monoclonal antibody as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier monoclonal indicates the character of the antibody as not being a mixture of discrete antibodies. Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones. It should be understood that the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this invention. In contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. In addition to their specificity, the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins. The modifier monoclonal indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by a variety of techniques, including, for example, the hybridoma method (e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567), phage display technologies (See, e.g., Clackson et al., Nature, 352: 624-628 (1991); Marks et al., J. Mol. Biol. 222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2): 299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al., J. Immunol. Methods 284(1-2): 119-132 (2004), and technologies for producing human or human-like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences (see, e.g., WO98/24893; WO96/34096; WO96/33735; WO91/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993); Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016; Marks et al., Bio. Technology 10: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild et al., Nature Biotechnol. 14: 845-851 (1996); Neuberger, Nature Biotechnol. 14: 826 (1996) and Lonberg and Huszar, Intern. Rev. Immunol. 13: 65-93 (1995).

(63) The monoclonal antibodies herein specifically include chimeric antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).

(64) See also the following review articles and references cited therein: Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1:105-115 (1998); Harris, Biochem. Soc. Transactions 23:1035-1038 (1995); Hudrle and Gross, Curr. Op. Biotech. 5:428-433 (1994).

(65) The term hypervariable region, HVR, or HV, when used herein refers to the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops. Generally, antibodies comprise six hypervariable regions; three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3). A number of hypervariable region delineations are in use and are encompassed herein. The Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are the most commonly used (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Chothia refers instead to the location of the structural loops (Chothia and Lesk J. Mol. Biol. 196:901-917 (1987)). The AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular's AbM antibody modeling software. The contact hypervariable regions are based on an analysis of the available complex crystal structures. The residues from each of these hypervariable regions are noted below.

(66) Loop Kabat AbM Chothia Contact

(67) L1 L24-L34 L24-L34 L26-L32 L30-L36

(68) L2 L50-L56 L50-L56 L50-L52 L46-L55

(69) L3 L89-L97 L89-L97 L91-L96 L89-L96

(70) H1 H31-H35B H26-H35B H26-H32 H30-H35B

(71) (Kabat Numbering)

(72) H1 H31-H35 H26-H35 H26-H32 H30-H35

(73) (Chothia Numbering)

(74) H2 H50-H65 H50-H58 H53-H55 H47-H58

(75) H3 H95-H102 H95-H102 H96-H101 H93-H101

(76) Hypervariable regions may comprise extended hypervariable regions as follows: 24-36 or 24-34 (L1), 46-56 or 50-56 or 49-56 (L2) and 89-97 or 89-96 (L3) in the VL and 26-35 (H1), 50-65 or 49-65 (H2) and 93-102, 94-102, or 95-102 (H3) in the VH. The variable domain residues are numbered according to Kabat et al., supra, for each of these definitions.

(77) Framework or FR residues are those variable domain residues other than the hypervariable region residues as herein defined.

(78) The term variable domain residue numbering as in Kabat or amino acid position numbering as in Kabat, and variations thereof, refers to the numbering system used for heavy chain variable domains or light chain variable domains of the compilation of antibodies in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or HVR of the variable domain. For example, a heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat) after residue 52 of H2 and inserted residues (e.g. residues 82a, 82b, and 82c, etc. according to Kabat) after heavy chain FR residue 82. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a standard Kabat numbered sequence.

(79) Single-chain Fv or scFv antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Generally, the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFv see Pluckthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994).

(80) The term diabodies refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO93/1161; and Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993).

(81) A human antibody is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.

(82) An affinity matured antibody is one with one or more alterations in one or more HVRs thereof which result in an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s). In one embodiment, an affinity matured antibody has nanomolar or even picomolar affinities for the target antigen. Affinity matured antibodies are produced by procedures known in the art. Marks et al. Bio/Technology 10:779-783 (1992) describes affinity maturation by VH and VL domain shuffling. Random mutagenesis of CDR and/or framework residues is described by: Barbas et al. Proc Nat. Acad. Sci. USA 91:3809-3813 (1994); Schier et al. Gene 169:147-155 (1995); Yelton et al. J. Immunol. 155:1994-2004 (1995); Jackson et al., J. Immunol. 154(7):3310-9 (1995); and Hawkins et al, J. Mol. Biol. 226:889-896 (1992).

(83) A blocking antibody or an antagonist antibody is one which inhibits or reduces biological activity of the antigen it binds. Certain blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.

(84) An agonist antibody, as used herein, is an antibody which mimics at least one of the functional activities of a polypeptide of interest.

(85) A disorder is any condition that would benefit from treatment with an antibody of the invention. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein include cancer.

(86) The terms cell proliferative disorder and proliferative disorder refer to disorders that are associated with some degree of abnormal cell proliferation. In one embodiment, the cell proliferative disorder is cancer.

(87) Tumor, as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms cancer, cancerous, cell proliferative disorder, proliferative disorder and tumor are not mutually exclusive as referred to herein.

(88) The terms cancer and cancerous generally refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth/proliferation. Examples of cancer include, but are not limited to, carcinoma, lymphoma (e.g., Hodgkin's and non-Hodgkin's lymphoma), blastoma, sarcoma, and leukemia. More particular examples of such cancers include squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, leukemia and other lymphoproliferative disorders, and various types of head and neck cancer.

(89) As used herein, the term antigen is defined as any substance capable of eliciting an immune response.

(90) As used herein, the term antigen specific refers to a property of a cell population such that supply of a particular antigen, or a fragment of the antigen, results in specific cell proliferation.

(91) As used herein, treatment refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing or decreasing inflammation and/or tissue/organ damage, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, antibodies of the invention are used to delay development of a disease or disorder.

(92) An individual or a subject is a vertebrate. In certain embodiments, the vertebrate is a mammal. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs, and horses), primates, mice and rats. In certain embodiments, the vertebrate is a human.

(93) Mammal for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. In certain embodiments, the mammal is human.

(94) An effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result.

(95) A therapeutically effective amount of a substance/molecule of the invention may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance/molecule, to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the substance/molecule are outweighed by the therapeutically beneficial effects. A prophylactically effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount would be less than the therapeutically effective amount.

(96) The term cytotoxic agent as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu), chemotherapeutic agents (e.g., methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents, enzymes and fragments thereof such as nucleolyticenzymes, antibiotics, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof, and the various antitumor or anticancer agents disclosed below. Other cytotoxic agents are described below. A tumoricidal agent causes destruction of tumor cells.

(97) A chemotherapeutic agent is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents such as thiotepa and CYTOXAN cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); delta-9-tetrahydrocannabinol (dronabinol, MARINOL); beta-lapachone; lapachol; colchicines; betulinic acid; a camptothecin (including the synthetic analogue topotecan (HYCAMTIN), CPT-11 (irinotecan, CAMPTOSAR), acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlomaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gamma1I and calicheamicin omegaI1 (see, e.g., Agnew, Chem. Intl. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2,2-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine (ELDISINE, FILDESIN); dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (Ara-C); thiotepa; taxoids, e.g., TAXOL paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), and TAXOTERE doxetaxel (Rhne-Poulenc Rorer, Antony, France); chloranbucil; gemcitabine (GEMZAR); 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine (VELBAN); platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine (ONCOVIN); oxaliplatin; leucovovin; vinorelbine (NAVELBINE); novantrone; edatrexate; daunomycin; aminopterin; ibandronate; topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoids such as retinoic acid; capecitabine (XELODA); pharmaceutically acceptable salts, acids or derivatives of any of the above; as well as combinations of two or more of the above such as CHOP, an abbreviation for a combined therapy of cyclophosphamide, doxorubicin, vincristine, and prednisolone, and FOLFOX, an abbreviation for a treatment regimen with oxaliplatin (ELOXATIN) combined with 5-FU and leucovovin.

(98) As used herein, treatment refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing or decreasing inflammation and/or tissue/organ damage, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, antibodies of the invention are used to delay development of a disease or disorder.

(99) An individual or a subject is a vertebrate. In certain embodiments, the vertebrate is a mammal. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs, and horses), primates, mice and rats. In certain embodiments, the vertebrate is a human.

(100) Mammal for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. In certain embodiments, the mammal is human.

(101) An effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result.

(102) A therapeutically effective amount of a substance/molecule of the invention may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance/molecule, to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the substance/molecule are outweighed by the therapeutically beneficial effects. A prophylactically effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount would be less than the therapeutically effective amount.

(103) The term cytotoxic agent as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu), chemotherapeutic agents (e.g., methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents, enzymes and fragments thereof such as nucleolyticenzymes, antibiotics, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof, and the various antitumor or anticancer agents disclosed below. Other cytotoxic agents are described below. A tumoricidal agent causes destruction of tumor cells.

(104) Administration in combination with one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

(105) Glycoantibodies

(106) The glycosylation of recombinant proteins produced from mammalian cells in culture is an important process in ensuring the effective use of therapeutic antibodies (Goochee et al., 1991; Jenkins and Curling, 1994). Mammalian cell culture delivers a heterogeneous mixture of glycosylation patterns which do not all have the same properties. Properties like safety, efficacy and the serum half-life of therapeutic proteins can be affected by these glycosylation patterns. We have successfully addressed the glycoform heterogeneity problem by the development of a novel class of monoclonal antibodies, named glycoantibodies.

(107) The term glycoantibodies was coined by the inventor, Dr. Chi-Huey Wong, to refer to a homogeneous population of monoclonal antibodies (preferably, therapeutic monoclonal antibodies) having a single, uniformed glycoform on Fc. The individual glycoantibodies comprising the homogeneous population are identical, bind to the same epitope, and contain the same Fc glycan with a well-defined glycan structure and sequence.

(108) Glycoantibodies may be generated from monoclonal antibodies (preferably, therapeutic monoclonal antibodies) commercially available or in the development. Monoclonal antibodies for therapeutic use can be humanized, human or chimeric. Examples of approved monoclonal antibodies for therapeutic use include, but not limited to, Muromomab, Abciximab, Rituximab, Daclizumab, Basiliximab, Palivizumab, Infliximab, Trastuzumab, Etanercept, Gemtuzumab, Alemtuzumab, Ibritomomab, Adalimumab, Alefacept, Omalizumab, Efalizumab, Cetuximab, Bevacizumab, Natalizumab, Ranibizumab, Panitumumab, Eculizumab and Certolizumab.

(109) Described herein are the functionally active glycoantibodies derived from therapeutic monoclonal antibodies by Fc glycoengineering. The glycoantibodies with optimized glycoforms exhibit more potent biological activities compared to the therapeutic monoclonal antibodies. It is contemplated that the glycoantibodies with optimized glycoforms may provide an alternative for therapeutic use.

(110) Anti-HER2 Glycoantibody (Anti-HER2 GAb)

(111) The HER2 gene is overexpressed or amplified in approximately 30% of breast cancers. Breast cancer patients with HER2 overexpression or amplification have shortened disease-free and overall survivals. The HER2 protein is thought to be a unique and useful target for antibody therapy of cancers overexpressing the HER2 gene. A monoclonal antibody anti-HER2, Trastuzumab (Herceptin), has been successfully used in therapy for malignant cancers relating to this target, which was approved by FDA in 1998 for the treatment of HER2 overexpressing breast cancer. A need remains for improved therapeutic antibodies against HER2 which are more effective in preventing and/or treating a range of diseases involving cells expressing HER2, including but not limited breast cancer.

(112) The present disclosure features a novel class of anti-HER2 antibodies, termed anti-HER2 glycoantibodies (anti-HER2 GAb). The anti-HER2 glycoantibodies can be generated from anti-HER2 monoclonal antibodies by Fc glycoengineering. The individual anti-HER2 glycoantibodies comprising the homogeneous population are identical and contain the same Fc glycan with a well-defined glycan structure and sequence. The anti-HER2 GAb according to the present invention specifically binds to the same epitope of a human HER2 antigen as its patent antibody.

(113) The term parental antibody as used herein refers to the anti-HER2 monoclonal antibody used to produce an anti-HER2 glycoantibody.

(114) The parental antibodies can be obtained by cell culturing such as mammalian cell culture, Pichia pastoris or insect cell lines. Preferrably, the parental antibodies are produced in mammalian cell culture. The parental antibodies may be FDA approved or in development. FDA approved anti-HER2 therapeutic antibodies include Trastuzumab (Herceptin), Lapatinib (Tykerb), Pertuzumab (Perjeta), Ado-trastuzumab emtansine (Kadcyla, Genentech).

(115) In some embodiments, the anti-HER2 GAb described herein comprise a heavy chain having the amino acid sequence set forth in SEQ ID NO: 1, and a light chain having the amino acid sequence set forth in SEQ ID NO: 2. In a preferred embodiment, the anti-HER2 GAb comprises a light chain sequence and a heavy chain sequence of Trastuzumab.

(116) Table 1 below shows the heavy chain and the light chain sequences of Trastuzumab.

(117) TABLE-US-00001 TABLE1 Trastuzumab AccessionNumber:DB00072 Source:http://www.drugbank.ca/drugs/DB00072 >AminoacidsequenceforTrastuzumablightchain DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPK LLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQ HYTTPPTFGQGTKVEIKRTVaAPSVFIFPPSDEQLKSGTASVVCL LNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC (SEQID:2) >AminoacidsequenceforTrastuzumabheavychain EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGL EWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAED TAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSS KSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK THTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVS HEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQD WLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRE EMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG SFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQID:1)

(118) In some embodiments, the N-glycan is attached to the Asn-297 of the Fc region.

(119) The N-glycans according to the invention have a common pentasaccharide core of Man.sub.3GlcNAc.sub.2 which is also referred to as trimannose core or pentasaccharide core, wherein Man refers to mannose, Glc refers to glucose, NAc refers to N-acetyl, and GlcNAc refers to N-acetylglucosamine.

(120) In some embodiments, the N-glycan has a biantennary structure.

(121) The N-glycan described herein may have intrachain substitutions comprising bisecting GlcNAc. When a glycan comprises a bisecting GlcNAc on the trimannose core, the structure is represented as Man.sub.3GlcNAc.sub.3. When a glycan comprises a core fucose attached to the trimannose core, the structure is represented as Man.sub.3GlcNAc.sub.2(F). The N-glycan may comprise one or more terminal sialic acids (e.g. N-acetylneuraminic acid). The structure represented as Sia refers to a terminal sialic acid. Sialylation may occur on either the 1-3 or 1-6 arm of the biantennary structures.

(122) In some embodiments, the N-glycan described herein comprises at least one 2-6 terminal sialic acid. In certain embodiments, the N-glycan comprises one 2-6 terminal sialic acid. In a preferred embodiment, the N-glycan comprises two 2-6 terminal sialic acids.

(123) In some embodiments, the N-glycan described herein comprises at least one 2-3 terminal sialic acid. In certain embodiments, the N-glycan comprises one 2-3 terminal sialic acid. In a preferred embodiment, the N-glycan comprises two 2-3 terminal sialic acids.

(124) In some embodiments, the N-glycan described herein comprises at least one galactose. In certain embodiments, the N-glycan comprises one galactose. In a preferred embodiment, the N-glycan comprises two galactoses.

(125) Preferrably, the N-glycan according to the disclosure is free of core fucose.

(126) FIGS. 8 through 11 show a table listing exemplary N-glycans of anti-HER2 glycoantibodies. Embodiments of the present disclosure may include or exclude any of the N-glycans listed herein.

(127) Biological Characteristic of Anti-HER2 Glycoantibodies

(128) Glycosylation on Fc can affect a variety of immunoglobulin effector-mediated functions, including ADCC, CDC and circulating half-life. ADCC enhancement is a key strategy for improving therapeutic antibody drug efficacy. It has the potential of lowering effective drug dosage for benefits of lower drug cost. The anti-HER2 glycoantibodies described herein can be characterized by functional properties. The anti-HER2 GAb has cell growth inhibitory activities including apoptosis against human HER2 expressing cells. In some embodiments, the anti-HER2 GAb exhibits more potent cell growth inhibitory activities as compared to its patent antibody.

(129) ADCC Activities of anti-HER2 Glycoantibodies

(130) The ADCC activity of the glycoantibody according to the invention is at least 3 fold increased, preferably at least 9 fold, more preferably at least 10 fold increased ADCC activity, preferably at least 12 fold increased ADCC activity, preferably at least 20 fold increased ADCC activity, most preferred at least 30 fold increased ADCC activity compared to the ADCC activity of the parental antibody.

(131) The ADCC lysis activity of the inventive glycoantibody can be measured in comparison to the parental antibody using target cancer cell lines such as SKBR5, SKBR3, LoVo, MCF7, OVCAR3 and/or Kato III.

(132) Table 3 lists exemplary enhanced ADCC activities of anti-HER2 GAbs as compared to Trastuzumab. Exemplary assays are described in the examples.

(133) TABLE-US-00002 TABLE 3 Anti-HER2 Trastuzumab GAb101 GAb104 GAb105 GAb107 GAb108 GAb111 ADCC 1 >30 >30 20~30 >10 5~10 1~5 (fold)

(134) A number of anti-HER2 GAbs described herein, in particular GAb101, and GAb104, exhibit enhanced ADCC activity compared to it parental antibody, Trastuzumab. It is contemplated that the glycoantibodies of the invention may exhibit superior effect as therapeutic agents for HER2-positive diseases, and an object of the present invention is to use the anti-HER2 GAb in development of therapeutic agents.

(135) CDC Activities of Anti-HER2 Glycoantibodies

(136) The glycoantibody described herein is surprisingly able to provide improved ADCC without affecting CDC. Exemplary CDC assays are described in the examples. In exemplary embodiments, ADCC of the glycoantibody is increased but other immunoglobulin-type effector functions such as complement-dependent cytoxicity (CDC) remain similar or are not significantly affected.

(137) Binding between FcRIII and Anti-HER2 Glycoantibodies

(138) Table 4 lists exemplary FcRIIIA binding of anti-HER2 GAbs and Herceptin.

(139) TABLE-US-00003 TABLE 4 Sample KD (M) Rmax (RU) Fold Herceptin 80~200 30.01 1-fold 101 1~25 44.98 >10X 104 1~25 55.68 >10X 111 35~100 41.54 1~5X 108 25~100 53.98 1~5X 107 20~90 39.88 3~10X 109 25~80 48.19 2~10X 110 70~150 18.15 1~5X 106 25~80 52.82 1~10X 103 15~70 59.89 4~10X 117 1~50 26.95 1~5X

(140) FcRIIIA binding may be measured using assays known in the art. Exemplary assays are described in the examples. The Fc receptor binding may be determined as the relative ratio of anti-HER2 GAb vs Trastuzumab. Fc receptor binding in exemplary embodiments is increased by at least 2.5-fold, 3-fold. 4-fold. 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold or 20-fold. 30-fold, 40-fold, 50-fold or higher.

(141) As compared to Trastuzumab, the binding data showed that the anti-HER2 GAbs, in particular GAb101 and GAb104, exhibit stronger binding affinity for the target molecule HER2.

(142) Taken together, anti-HER2 GAbs, in particular GAb101, and GAb104, exhibit enhanced ADCC activity and stronger FcRIIIA binding affinity as compared to Trastuzumab. It is contemplated that the glycoantibodies of the invention may provide a superior clinical response either alone or, preferably, in a composition comprising two or more such antibodies, and optionally in combination with other treatments such as chemotherapy. It is contemplated that the ADCC-enhanced anti-HER2 glycoantibody may provide an alternative therapeutic for HER2-positive diseases. The glycoantibodies of the present invention advantageously can be used to alter current routes of administration and current therapeutic regimens, as their increased effector function means they can be dosed at lower concentrations and with less frequency, thereby reducing the potential for antibody toxicity and/or development of antibody tolerance. Furthermore, their improved effector function yields new approaches to treating clinical indications that have previously been resistant or refractory to treatment with the corresponding anti-HER2 monoclonal antibody produced in recombinant host systems.

(143) Preparation of Anti-HER2 GAb

(144) The anti-HER2 glycoantibodies of the invention can be produced by Fc glycoengineering from anti-HER2 monoclonal antibodies (parental antibodies) commercially available or in the preclinical or clinical development. Preferrably, the monoclonal antibodies are therapeutic monoclonal antibodies. Fc glycoengineering may be performed enzymatically or chemoenzymatically. In a preferred embodiment, the parental antibody is Trastuzumab.

(145) The N-glycans in the glycoantibodies of the invention are preferrably defucosylated.

(146) Defucosylation of N-glycans is a process to remove core fucoses in N-glycans of the Fc domains. Defucosylation can be employed enzymatically. Since N-glycans are embedded between two Fc domains, the enzymatic defucosylation efficiency is much lower due to steric hindrance, i.e., access of fucosidase to fucose residues is blocked by portions of the Fc domains.

(147) Many -fucosidases are known in the art. Examples include -fucosidases from Turbo comutus, Charonia lampas, Bacillus fulminans, Aspergillus niger, Clostridium perfringens, Bovine kidney (Glyko), chicken liver (Tyagarajan et al., 1996, Glycobiology 6:83-93) and -fucosidase II from Xanthomonas manihotis (Glyko, PROzyme). Many varieties of fucosidase are also commercially available (Glyko, Novato, Calif.; PROzyme, San Leandro, Calif.; Calbiochem-Novabiochem Corp., San Diego, Calif.; among others). However, none of -fucosidases are known to efficiently remove the core fucose from N-linked glycans.

(148) WO 2013/12066 disclosed the defucosylation of (Fucl, 6)GlcNAc-Rituximab by an -fucosidase from bovine kidney. As described in WO 2013/12066, a reaction mixture of (Fucl, 6)GlcNAc-Rituximab was incubated with -fucosidase from bovine kidney (commercially available from Prozyme) at 37 C. for 20 days to completely remove the fucose in (Fucl, 6)GlcNAc-Rituximab.

(149) Thermal instability of immunoglobulin is known in the art (Vermeer et al., Biophys J. January 78: 394-404 (2000)). The Fab fragment is most sensitive to heat treatment, whereas the Fc fragment is most sensitive to decreasing pH. To examine the thermal stability and functional activity of the antibody, we performed the same experiment as described in WO 2013/12066, and found the antibody lost about 10% binding affinity to CD20 after thermal treatment at 37 C. for 3 days. Furthermore, we found the antibody lost about 20% binding affinity to CD20 after thermal treatment at 37 C. for 7 days. It is contemplated that the antibody will significantly lose the binding affinity to CD20 after prolonged thermal treatment, such as at 37 C. for 20 days, as described in WO 2013/12066.

(150) In our attempts to synthesize the glycoantibodies with improved therapeutic values, we unexpectedly discovered a Bacteroides fragilis -fucosidase (GenBank accession no. YP_212855.1) that is capable of efficiently removing fucose residues from N-linked glycans. Efficient defucosylation has been successfully achieved using the specific enzyme. Importantly, the efficiency of making the glycoantibodies of the invention has been valuably improved by the use of the specific -fucosidase that yields a facile defucosylation of N-glycans, as illustrated in FIG. 1.

(151) Accordingly, the present invention provides a composition of the -fucosidase, and an improved method for removing core fucoses of N-glycans using the -fucosidase. The -fucosidase comprises a polypeptide having an amino acid sequence having at least 80%, 85% 90%, 95%, 98% or 99% identity to the sequences of SEQ ID NO: 5 or variants thereof. The improved method of defucosylation comprises contacting an antibody with an -fucosidase, and in which the -fucosidase comprises a polypeptide having an amino acid sequence having at least 80%, 85%, 90%, 95%, 98% or 99% identity to the sequences of SEQ ID NO: 5, a variant or a fragment thereof.

(152) Described herein includes an improved method for making an anti-HER2 glycoantibody, the method comprising the steps of (a) contacting an anti-HER2 monoclonal antibody with an -fucosidase and at least one endoglycosidase, thereby yielding a defucosylated antibody having a single N-acetylglucosamine (GlcNAc), and (b) adding a carbohydrate moiety to GlcNAc under suitable conditions.

(153) In some embodiments, the anti-HER2 monoclonal antibody is Trastuzumab.

(154) Endoglycosidase is used to trim off the variable portions of an oligosaccharide in N-glycan. Examples of endoglycosidases used herein include, but not limited to, EndoA, EndoF, EndoF1, EndoF2, EndoH, EndoM, EndoS, and variants thereof.

(155) The -fucosidase according to the method of the invention comprises a polypeptide having an amino acid sequence having at least 85% identity to the sequences of SEQ ID NO: 5, a functional variant thereof.

(156) In some embodiments, the -fucosidase comprises a polypeptide having an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identity to the sequences of SEQ ID NO: 5, a variant or a fragment thereof.

(157) In certain embodiments, the -fucosidase is a recombinant Bacteroides -fucosidase.

(158) TABLE-US-00004 TABLE5 QQKYQPTEANLKARSEFQDNKFGIFLHWGLYAMLATGEWT MTNNNLNYKEYAKLAGGFYPSKFDADKWVAAIKASGAKYICFTTRHHEGF SMFDTKYSDYNIVKATPFKRDVVKELADACAKHGIKLHFYYSHIDWYRED APQGRTGRRTGRPNPKGDWKSYYQFMNNQLTELLTNYGPIGAIWFDGWWD QDINPDFDWELPEQYALIHRLQPACLVGNNHHQTPFAGEDIQIFERDLPG ENTAGLSGQSVSHLPLETCETMNGMWGYKITDQNYKSTKTLIHYLVKAAG KDANLLMNIGPQPDGELPEVAVQRLKEVGEWMSKYGETIYGTRGGLVAPH DWGVTTQKGNKLYVHILNLQDKALFLPIVDKKVKKAVVFADKTPVRFTKN KEGIVLELAKVPTDVDYVVELTID (SEQID:5)

(159) Step (a) in the method of the invention leads to a defucosylated antibody having a single N-acetylglucosamine (GlcNAc). Subsequent enzyme-mediated glycosylation using a transglycosylase is performed to add a designated carbohydrate moiety to GlcNAc and extend the sugar chain. A homogenous population of glycoantibodies can therefore be produced. Examples of transglycosylases as described herein include, but not limited to, EndoA, EndoF, EndoF1, EndoF2, EndoH, EndoM, EndoS, and variants thereof.

(160) In some embodiments, the carbohydrate moiety according to the method the invention is selected from the group consisting of Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-6)GalGlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-3)GalGlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-6)GalGlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-3)GalGlcNAc.sub.3Man.sub.3GlcNAc, Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, GalGlcNAc.sub.2Man.sub.3GlcNAc, GalGlcNAc.sub.3Man.sub.3GlcNAc, GlcNAc.sub.3Man.sub.3GlcNAc, GlcNAc.sub.2Man.sub.3GlcNAc, GlcNAcMan.sub.3GlcNAc and Man.sub.3GlcNAc.

(161) In preferred embodiments, the carbohydrate moiety is selected from the group consisting of Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia.sub.2(2-3/2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia.sub.2(2-6/2-3)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-3)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-6)Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-3)Gal.sub.2GlcNAcMan.sub.3GlcNAc, Sia(2-6)GalGlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-3)GalGlcNAc.sub.2Man.sub.3GlcNAc, Sia(2-6)GalGlcNAc.sub.3Man.sub.3GlcNAc, Sia(2-3)GalGlcNAc.sub.3Man.sub.3GlcNAc, Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc and Gal.sub.2GlcNAc.sub.3Man.sub.3GlcNAc.

(162) Step (b) in the method of the invention leads to sugar chain extension. One method for sugar chain extension is through an enzyme-catalyzed glycosylation reaction. It is well known in the art that glycosylation using a sugar oxazoline as the sugar donor among the enzyme-catalyzed glycosylation reactions is useful for synthesizing oligosaccharides because the glycosylation reaction is an addition reaction and advances without any accompanying elimination of acid, water, or the like. (Fujita, et al., Biochim. Biophys. Acta 2001, 1528, 9-14)

(163) In some embodiments, the carbohydrate moiety is a sugar oxazoline.

(164) Suitable conditions also include incubation of the reaction mixture for at least 20 minutes, 30 minutes, 40 minutes, 50 minutes, 60 minutes, 70 minutes, 80 minutes, 90 minutes or 100 minutes, preferably less than 60 minutes. Incubation preferably takes place at room temperature, more preferably at approximately 20 C., 25 C., 30 C., 35 C., 40 C. or 45 C., and most preferably at approximately 37 C.

(165) It will be understood that the polypeptide of the -fucosidase of the invention may be derivatized or modified to assist with their isolation or purification. Thus, in one embodiment of the invention, the polypeptide for use in the invention is derivatized or modified by addition of a ligand which is capable of binding directly and specifically to a separation means. Alternatively, the polypeptide is derivatized or modified by addition of one member of a binding pair and the separation means comprises a reagent that is derivatized or modified by addition of the other member of a binding pair. Any suitable binding pair can be used. In a preferred embodiment where the polypeptide for use in the invention is derivatized or modified by addition of one member of a binding pair, the polypeptide is preferably histidine-tagged or biotin-tagged. Typically the amino acid coding sequence of the histidine or biotin tag is included at the gene level and the proteins are expressed recombinantly in E. coli. The histidine or biotin tag is typically present at one end of the polypeptide, either at the N-terminus or at the C-terminus. The histidine tag typically consists of six histidine residues (SEQ ID NO: 6), although it can be longer than this, typically up to 7, 8, 9, 10 or 20 amino acids or shorter, for example 5, 4, 3, 2 or 1 amino acids. Furthermore, the histidine tag may contain one or more amino acid substitutions, preferably conservative substitutions as defined above.

(166) Variant polypeptide as described herein are those for which the amino acid sequence varies from that in SEQ ID NO: 5, but exhibit the same or similar function of the enzyme comprising the polypeptide having an amino acid sequence of SEQ ID NO: 5.

(167) As used herein percent (%) sequence identity with respect to a sequence is defined as the percentage of amino acid residues in a candidate polypeptide sequence that are identical with the amino acid residues in the reference polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.

(168) Some preferred embodiments of the invention are demonstrated in the examples.

(169) Pharmaceutical Compositions and Formulations

(170) After preparation of the anti-HER2 GAb as described herein, a pre-lyophilized formulation can be produced. The anti-HER2 GAb for preparing the formulation is preferably essentially pure and desirably essentially homogeneous (i.e. free from contaminating proteins etc). Essentially pure protein means a composition comprising at least about 90% by weight of the protein, based on total weight of the composition, preferably at least about 95% by weight. Essentially homogeneous protein means a composition comprising at least about 99% by weight of protein, based on total weight of the composition. In certain embodiments, the protein is an antibody.

(171) The amount of anti-HER2 GAb in the pre-lyophilized formulation is determined taking into account the desired dose volumes, mode(s) of administration etc. Where the protein of choice is an intact antibody (a full-length antibody), from about 2 mg/mL to about 50 mg/mL, preferably from about 5 mg/mL to about 40 mg/mL and most preferably from about 20-30 mg/mL is an exemplary starting protein concentration. The protein is generally present in solution. For example, the protein may be present in a pH-buffered solution at a pH from about 4-8, and preferably from about 5-7. Exemplary buffers include histidine, phosphate, Tris, citrate, succinate and other organic acids. The buffer concentration can be from about 1 mM to about 20 mM, or from about 3 mM to about 15 mM, depending, for example, on the buffer and the desired isotonicity of the formulation (e.g. of the reconstituted formulation). The preferred buffer is histidine in that, as demonstrated below, this can have lyoprotective properties. Succinate was shown to be another useful buffer.

(172) The lyoprotectant is added to the pre-lyophilized formulation. In preferred embodiments, the lyoprotectant is a non-reducing sugar such as sucrose or trehalose. The amount of lyoprotectant in the pre-lyophilized formulation is generally such that, upon reconstitution, the resulting formulation will be isotonic. However, hypertonic reconstituted formulations may also be suitable. In addition, the amount of lyoprotectant must not be too low such that an unacceptable amount of degradation/aggregation of the protein occurs upon lyophilization. Where the lyoprotectant is a sugar (such as sucrose or trehalose) and the protein is an antibody, exemplary lyoprotectant concentrations in the pre-lyophilized formulation are from about 10 mM to about 400 mM, and preferably from about 30 mM to about 300 mM, and most preferably from about 50 mM to about 100 mM.

(173) The ratio of protein to lyoprotectant is selected for each protein and lyoprotectant combination. In the case of an antibody as the protein of choice and a sugar (e.g., sucrose or trehalose) as the lyoprotectant for generating an isotonic reconstituted formulation with a high protein concentration, the molar ratio of lyoprotectant to antibody may be from about 100 to about 1500 moles lyoprotectant to 1 mole antibody, and preferably from about 200 to about 1000 moles of lyoprotectant to 1 mole antibody, for example from about 200 to about 600 moles of lyoprotectant to 1 mole antibody.

(174) In preferred embodiments of the invention, it has been found to be desirable to add a surfactant to the pre-lyophilized formulation. Alternatively, or in addition, the surfactant may be added to the lyophilized formulation and/or the reconstituted formulation. Exemplary surfactants include nonionic surfactants such as polysorbates (e.g. polysorbates 20 or 80); poloxamers (e.g. poloxamer 188); Triton; sodium dodecyl sulfate (SDS); sodium laurel sulfate; sodium octyl glycoside; lauryl-, myristyl-, linoleyl-, or stearyl-sulfobetaine; lauryl-, myristyl-, linoleyl- or stearyl-sarcosine; linoleyl-, myristyl-, or cetyl-betaine; lauroamidopropyl-, cocamidopropyl-, linoleamidopropyl-, myristamidopropyl-, palnidopropyl-, or isostearamidopropyl-betaine (e.g. lauroamidopropyl); myristamidopropyl-, palmidopropyl-, or isostearamidopropyl-dimethylamine; sodium methyl cocoyl-, or disodium methyl oleyl-taurate; and the MONAQUAT series (Mona Industries, Inc., Paterson, N.J.), polyethyl glycol, polypropyl glycol, and copolymers of ethylene and propylene glycol (e.g. Pluronics, PF68 etc). The amount of surfactant added is such that it reduces aggregation of the reconstituted protein and minimizes the formation of particulates after reconstitution. For example, the surfactant may be present in the pre-lyophilized formulation in an amount from about 0.001-0.5%, and preferably from about 0.005-0.05%.

(175) In certain embodiments of the invention, a mixture of the lyoprotectant (such as sucrose or trehalose) and a bulking agent (e.g. mannitol or glycine) is used in the preparation of the pre-lyophilization formulation. The bulking agent may allow for the production of a uniform lyophilized cake without excessive pockets therein etc.

(176) Other pharmaceutically acceptable carriers, excipients or stabilizers such as those described in Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980) may be included in the pre-lyophilized formulation (and/or the lyophilized formulation and/or the reconstituted formulation) provided that they do not adversely affect the desired characteristics of the formulation. Acceptable carriers, excipients or stabilizers are nontoxic to recipients at the dosages and concentrations employed and include; additional buffering agents; preservatives; co-solvents; antioxidants including ascorbic acid and methionine; chelating agents such as EDTA; metal complexes (e.g. Zn-protein complexes); biodegradable polymers such as polyesters; and/or salt-forming counterions such as sodium.

(177) The pharmaceutical compositions and formulations described herein are preferably stable. A stable formulation/composition is one in which the antibody therein essentially retains its physical and chemical stability and integrity upon storage. Various analytical techniques for measuring protein stability are available in the art and are reviewed in Peptide and Protein Drug Delivery, 247-301, Vincent Lee Ed., Marcel Dekker, Inc., New York, N.Y., Pubs. (1991) and Jones, A. Adv. Drug Delivery Rev. 10: 29-90 (1993). Stability can be measured at a selected temperature for a selected time period.

(178) The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to, or following, lyophilization and reconstitution. Alternatively, sterility of the entire mixture may be accomplished by autoclaving the ingredients, except for protein, at about 120 C. for about 30 minutes, for example.

(179) After the protein, lyoprotectant and other optional components are mixed together, the formulation is lyophilized. Many different freeze-dryers are available for this purpose such as Hull50 (Hull, USA) or GT20 (Leybold-Heraeus, Germany) freeze-dryers. Freeze-drying is accomplished by freezing the formulation and subsequently subliming ice from the frozen content at a temperature suitable for primary drying. Under this condition, the product temperature is below the eutectic point or the collapse temperature of the formulation. Typically, the shelf temperature for the primary drying will range from about 30 to 25 C. (provided the product remains frozen during primary drying) at a suitable pressure, ranging typically from about 50 to 250 mTorr. The formulation, size and type of the container holding the sample (e.g., glass vial) and the volume of liquid will mainly dictate the time required for drying, which can range from a few hours to several days (e.g. 40-60 hrs). A secondary drying stage may be carried out at about 0-40 C., depending primarily on the type and size of container and the type of protein employed. However, it was found herein that a secondary drying step may not be necessary. For example, the shelf temperature throughout the entire water removal phase of lyophilization may be from about 15-30 C. (e.g., about 20 C.). The time and pressure required for secondary drying will be that which produces a suitable lyophilized cake, dependent, e.g., on the temperature and other parameters. The secondary drying time is dictated by the desired residual moisture level in the product and typically takes at least about 5 hours (e.g. 10-15 hours). The pressure may be the same as that employed during the primary drying step. Freeze-drying conditions can be varied depending on the formulation and vial size.

(180) In some instances, it may be desirable to lyophilize the protein formulation in the container in which reconstitution of the protein is to be carried out in order to avoid a transfer step. The container in this instance may, for example, be a 3, 5, 10, 20, 50 or 100 cc vial. As a general proposition, lyophilization will result in a lyophilized formulation in which the moisture content thereof is less than about 5%, and preferably less than about 3%.

(181) At the desired stage, typically when it is time to administer the protein to the patient, the lyophilized formulation may be reconstituted with a diluent such that the protein concentration in the reconstituted formulation is at least 50 mg/mL, for example from about 50 mg/mL to about 400 mg/mL, more preferably from about 80 mg/mL to about 300 mg/mL, and most preferably from about 90 mg/mL to about 150 mg/mL. Such high protein concentrations in the reconstituted formulation are considered to be particularly useful where subcutaneous delivery of the reconstituted formulation is intended. However, for other routes of administration, such as intravenous administration, lower concentrations of the protein in the reconstituted formulation may be desired (for example from about 5-50 mg/mL, or from about 10-40 mg/mL protein in the reconstituted formulation). In certain embodiments, the protein concentration in the reconstituted formulation is significantly higher than that in the pre-lyophilized formulation. For example, the protein concentration in the reconstituted formulation may be about 2-40 times, preferably 3-10 times and most preferably 3-6 times (e.g. at least three fold or at least four fold) that of the pre-lyophilized formulation.

(182) Reconstitution generally takes place at a temperature of about 25 C. to ensure complete hydration, although other temperatures may be employed as desired. The time required for reconstitution will depend, e.g., on the type of diluent, amount of excipient(s) and protein. Exemplary diluents include sterile water, bacteriostatic water for injection (BWFI), a pH buffered solution (e.g. phosphate-buffered saline), sterile saline solution, Ringer's solution or dextrose solution. The diluent optionally contains a preservative. Exemplary preservatives have been described above, with aromatic alcohols such as benzyl or phenol alcohol being the preferred preservatives. The amount of preservative employed is determined by assessing different preservative concentrations for compatibility with the protein and preservative efficacy testing. For example, if the preservative is an aromatic alcohol (such as benzyl alcohol), it can be present in an amount from about 0.1-2.0% and preferably from about 0.5-1.5%, but most preferably about 1.0-1.2%. Preferably, the reconstituted formulation has less than 6000 particles per vial which are >10 m size.

(183) Immunoconjugates

(184) 1 In another aspect, the invention provides immunoconjugates, or antibody-drug conjugates (ADC), comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).

(185) The use of antibody-drug conjugates for the local delivery of cytotoxic or cytostatic agents, i.e. drugs to kill or inhibit tumor cells in the treatment of cancer (Syrigos and Epenetos (1999) Anticancer Research 19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drg Del. Rev. 26:151-172; U.S. Pat. No. 4,975,278) allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated (Baldwin et al., (1986) Lancet pp. (Mar. 15, 1986):603-05; Thorpe, (1985) Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review, in Monoclonal Antibodies '84: Biological And Clinical Applications, A. Pinchera et al. (ed.s), pp. 475-506). Maximal efficacy with minimal toxicity is sought thereby. Both polyclonal antibodies and monoclonal antibodies have been reported as useful in these strategies (Rowland et al., (1986) Cancer Immunol. Immunother., 21:183-87). Drugs used in these methods include daunomycin, doxorubicin, methotrexate, and vindesine (Rowland et al., (1986) supra). Toxins used in antibody-toxin conjugates include bacterial toxins such as diphtheria toxin, plant toxins such as ricin, small molecule toxins such as geldanamycin (Mandler et al (2000) Jour. of the Nat. Cancer Inst. 92(19):1573-1581; Mandler et al (2000) Bioorganic & Med. Chem. Letters 10:1025-1028; Mandler et al (2002) Bioconjugate Chem. 13:786-791), maytansinoids (EP 1391213; Liu et al., (1996) Proc. Natl. Acad. Sci. USA 93:8618-8623), and calicheamicin (Lode et al (1998) Cancer Res. 58:2928; Hinman et al (1993) Cancer Res. 53:3336-3342). The toxins may affect their cytotoxic and cytostatic effects by mechanisms including tubutin binding, DNA binding, or topoisomerase inhibition. Some cytotoxic drugs tend to be inactive or less active when conjugated to large antibodies or protein receptor ligands.

(186) Antibody Derivatives

(187) Antibodies of the invention can be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available. In one embodiment, the moieties suitable for derivatization of the antibody are water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody may vary, and if more than one polymer is attached, the polymers can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the antibody derivative will be used in a therapy under defined conditions, etc.

(188) In another embodiment, conjugates of an antibody and nonproteinaceous moiety that may be selectively heated by exposure to radiation are provided. In one embodiment, the nonproteinaceous moiety is a carbon nanotube (Kam et al., Proc. Natl. Acad. Sci. 102: 11600-11605 (2005)). The radiation may be of any wavelength, and includes, but is not limited to, wavelengths that do not harm ordinary cells, but which heat the nonproteinaceous moiety to a temperature at which cells proximal to the antibody-nonproteinaceous moiety are killed.

(189) Therapeutic Applications

(190) Trastuzumab (Herceptin) is widely used and known in the art for the treatment of patients with early as well as metastatic breast cancer whose tumors overexpress HER2 protein or have HER 2 gene amplification. In the art, the treatment of breast cancer patients with Herceptin/Trastuzumab is, for example, recommended and routine for patients having HER2-positive disease. HER2-positive disease in breast cancer is present if a high HER2 (protein) expression level detected by immunohistochemical methods (e.g. HER2 (+++) or HER2 gene amplification (e.g. a HER2 gene copy number higher than 4 copies of the HER2 gene per tumor cell) or both is found in samples obtained from the patients such as breast tissue biopsies or breast tissue resections or in tissue derived from metastatic sites.

(191) ADCC-enhanced anti-HER2 glycoantibodies provides an alternative therapeutic for treating HER2-expressing tumors. The glycoantibodies of the present invention advantageously can be used to alter current routes of administration and current therapeutic regimens, as their increased effector function means they can be dosed at lower concentrations and with less frequency, thereby reducing the potential for antibody toxicity and/or development of antibody tolerance. Furthermore, their improved effector function yields new approaches to treating clinical indications that have previously been resistant or refractory to treatment with the corresponding anti-HER2 monoclonal antibody produced in recombinant host systems.

(192) Accordingly, the present disclosure relates to a method for treating a patient having a HER2-expressing tumor comprising administering to the patient an effective amount of the glycoantibody described herein. In a preferred aspect, the present disclosure provides a method for treating breast cancer.

(193) The composition described above can be a pharmaceutical composition, which can further comprise a pharmaceutically acceptable carrier.

(194) The composition can be delivered by administering the composition to a subject in need thereof (e.g., a human patient having or suspected of having cancer). In some embodiments, the anti-cancer agent is delivered to a subject in an amount effective in treating cancer. In other embodiments, a detectable label, preferably an agent suitable for cancer imaging, is delivered to a subject (e.g., a human patient having or suspected of having a solid tumor) in an amount effective in detecting cancer cells and/or cancerous tissues.

(195) An antibody that induces apoptosis is one which induces programmed cell death as determined by binding of annexin V, fragmentation of DNA, cell shrinkage, dilation of endoplasmic reticulum, cell fragmentation, and/or formation of membrane vesicles (called apoptotic bodies). Preferably the cell is an infected cell. Various methods are available for evaluating the cellular events associated with apoptosis. For example, phosphatidyl serine (PS) translocation can be measured by annexin binding; DNA fragmentation can be evaluated through DNA laddering; and nuclear/chromatin condensation along with DNA fragmentation can be evaluated by any increase in hypodiploid cells. Preferably, the antibody that induces apoptosis is one that results in about 2 to 50 fold, preferably about 5 to 50 fold, and most preferably about 10 to 50 fold, induction of annexin binding relative to untreated cell in an annexin binding assay.

(196) Antibody effector functions refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.

(197) Antibody-dependent cell-mediated cytotoxicity or ADCC refers to a form of cytotoxicity in which secreted Ig bound to Fc receptors (FcRs) present on certain cytotoxic cells (e.g., Natural Killer (NK) cells, neutrophils, and macrophages) enable these cytotoxic effector cells to bind specifically to an antigen-bearing target cell and subsequently kill the target cell with cytotoxins. The antibodies arm the cytotoxic cells and are required for such killing. The primary cells for mediating ADCC, NK cells, express FcRIII only, whereas monocytes express FcRI, FcRII and FcRII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). To assess ADCC activity of a molecule of interest, an in vitro ADCC assay, such as that described in U.S. Pat. Nos. 5,500,362 or 5,821,337 may be performed. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al., Proc. Natl. Acad. Sci. (USA) 95:652-656 (1998).

(198) Fc receptor or FcR describes a receptor that binds to the Fc region of an antibody. In certain embodiments, the FcR is a native sequence human FcR. Moreover, a preferred FcR is one that binds an IgG antibody (a gamma receptor) and includes receptors of the FcRI, FcRII, and FcRIII subclasses, including allelic variants and alternatively spliced forms of these receptors. FcRII receptors include FcRIIA (an activating receptor) and FcRIIB (an inhibiting receptor), which have similar amino acid sequences that differ primarily in the cytoplasmic domains thereof. Activating receptor FcRIIA contains an immunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmic domain. Inhibiting receptor FcRIIB contains an immunoreceptor tyrosine-based inhibition motif (ITIM) in its cytoplasmic domain. (reviewed by M. Daeron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med. 126:330-41 (1995). Other FcRs, including those to be identified in the future, are encompassed by the term FcR herein. The term also includes the neonatal receptor, FcRn, which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)).

(199) Human effector cells are leukocytes that express one or more FcRs and perform effector functions. Preferably, the cells express at least FcRIII and perform ADCC effector function. Examples of human leukocytes that mediate ADCC include PBMC, NK cells, monocytes, cytotoxic T cells and neutrophils; with PBMCs and NK cells being preferred. The effector cells may be isolated from a native source, e.g., from blood.

(200) 21 Complement dependent cytotoxicity or CDC refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (C1q) to antibodies (of the appropriate subclass) that are bound to their cognate antigen. To assess complement activation, a CDC assay, e.g., as described in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), may be performed.

(201) Treating or treatment or alleviation refers to both therapeutic treatment and prophylactic or preventative measures; wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented. A subject or mammal is successfully treated for an infection if, after receiving a therapeutic amount of an antibody according to the methods of the present invention, the patient shows observable and/or measurable reduction in or absence of one or more of the following: reduction in the number of infected cells or absence of the infected cells; reduction in the percent of total cells that are infected; and/or relief to some extent, one or more of the symptoms associated with the specific infection; reduced morbidity and mortality, and improvement in quality of life issues. The above parameters for assessing successful treatment and improvement in the disease are readily measurable by routine procedures familiar to a physician.

(202) The term therapeutically effective amount refers to an amount of an antibody or a drug effective to treat a disease or disorder in a subject or mammal See preceding definition of treating.

(203) Administration in combination with one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

(204) Carriers as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN polyethylene glycol (PEG), and PLURONICS.

(205) The details of one or more embodiments of the invention are set forth in the description below. Other features or advantages of the present invention will be apparent from the following drawings and detailed description of several embodiments, and also from the appending claims.

(206) The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

EXAMPLES

(207) Exemplary General Procedures

(208) Method A: Glycosylation by Thio-Glycan Donor

(209) To activate molecular sieves MS-4 for glycosylation, it was connected to vacuum system and heated for 1 hour. After the activated molecular sieves was cooled to room temperature, it was added to a flask containing Donor (1.52.0 eq. for one position glycosylation) and Acceptor (1.0 eq.). Dichloromethane was added to the mixture, and then the solution was stirred at room temperature for 3 h. N-iodosuccinimide (NIS, 1.7<2.2 eq.) and trimethylsilyl trifluoromethanesulfonate (TMSOTf, 0.1 eq.) were added to the solution on 78 C., and then the solution was stirred at 20 C. Reaction was monitored by thin-layer chromatography (TLC) analysis, which was carried out on glass-backed silica gel plates (Merck DC Kieselgel 60F.sub.234) and visualized by UV light (254 nm) and acidic ceric ammonium molybdate. After the acceptor was consumed completely, the reaction was quenched with sat. NaHCO.sub.3(aq), and 20% Na.sub.2S.sub.2O.sub.3, and then the mixture was filtered through a pad of celite. After the aqueous layer was extracted with two portions of dichloromethane, the combined organic layers were washed with brine, dried over MgSO.sub.4, and concentrated. The crude was purified by silica gel column chromatography (toluene/ethyl acetate as elution system) to give product (the yield was shown on the scheme).

(210) Method B: Glycosylation by Fluoride-Glycan Donor

(211) A mixture of silver triflate (5 eq.), bis (cyclopentadienyl) hafnium dichloride (3.5 eq.) and 4A activated molecular sieves in dry toluene was stirred at room temperature for 1 h. The reaction mixture was then cooled to 50 C., a solution of acceptor (1.0 eq.) and donor (1.21.5 eq.) in toluene was added. The mixture was stirred at 10 C. for 2-8 h. After TLC indicated complete consumption of acceptor, the reaction was quenched with Et.sub.3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO.sub.3, and a brine solution. The organic layers was dried over Na.sub.2SO.sub.4 and concentrated in vacuo. The crude was purified by silica gel column chromatography (toluene/ethyl acetate as elution system) to give product (the yield was shown on the scheme).

(212) Method C: Deprotection of O-Acetyl

(213) NaOMe (0.25 eq.) was added to solution of starting material (1.0 eq.) in THF/Methanol (2/3). Reaction was stirred at room temperature and monitored by TLC analysis. After the acetyl group was de-protected completely, the solution was neutralized by IR-120, filtered, and concentrated. The crude was purified by silica gel column chromatography (hexanes/ethyl acetate as elution system) to give product (the yield was shown on the scheme).

(214) Method D: Deprotection of O-Troc

(215) Zn powder (20 eq.) and acetic acid (0.2 eq.) were added to solution of starting material (1.0 eq.) in THF. Reaction was stirred at room temperature and monitored by thin-layer chromatography (TLC) analysis. After the Troc group was de-protected completely, the solution was filtered, and concentrated. The crude was purified by silica gel column chromatography (hexanes/ethyl acetate as elution system) to give product (the yield was shown on the scheme).

(216) Method E: Deprotection of Benzylidene

(217) p-Toluenesulfonic acid (pTSA, 1.5 eq.) was added to solution of starting material (1.0 eq.) in ACN/MeOH (2/1). Reaction was stirred at room temperature and monitored by thin-layer chromatography (TLC) analysis. After the benzylidene group was removed completely, the reaction was quenched by trimethylamine and then concentrated. The crude was purified by silica gel column chromatography (hexanes/ethyl acetate as elution system) to give product (the yield was shown on the scheme).

(218) Method F: Global Deprotection

(219) A mixture of protected oligosaccharides (50 mmol) and 10 mL of ethylene diamine: nBuOH (1/4) were stirred at 90 C. overnight. Volatiles were evaporated, and crude was reacted with 10 mL Ac.sub.2O/pyridine (1/2) overnight. The solvents were removed using high vacuum, and the product was purified by flash column chromatography (acetone/toluene as elute system). The products were de-acetylated using sodium methoxide in MeOH (10 mL) overnight Reactions were neutralized by using IR-120, then, filtered and concentrated in vacuum The residues were purified by flash column chromatography (acetone/toluene as elute system). The products were dissolved in 10 mL MeOH:H.sub.2O:HCOOH (6/3/1), Pd(OH).sub.2 (50% by weight) was added, and the reactions were hydrogenated overnight. The reaction mixtures were filtered through celite and concentrated in vacuo. The residues were purified by G-15 gel column chromatography using water as eluent. The products were lypholysed to get white color powders (the yield was shown on the scheme).

(220) Method G: Enzymatic (2,6)-Sialylation

(221) Starting materials (5 mol), CTP (1 mol), Neu5Ac (9.5 mol), PEP (10 mol), -2,6 sialyltransferase (200 L, estimated concentration of 2 mg/L), CMK (80 units), PK (40 units), and PPA (40 units) were dissolved in 50 mol sodium cacodylate (pH 7.4) containing 1% BSA (130 L). The reactions were incubated at 37 C. with gentle agitation for 2d. The products were purified by using G-15 gel chromatography (eluent H.sub.2O) to afford the desired products as white solid after lyophilization.

(222) FIG. 12 shows the building blocks for glycosylation. FIGS. 13-18 show schemes for synthesizing asymmetric N-glycans of this disclosure.

Example 1: Generation of Exemplary Anti-HER2 GAbs

(223) Anti-HER2 GAb301

(224) The complete removal of N-linked glycan at Asn.sup.297 from Fc region of Trastuzumab (Herceptin) is achieved by means of PNGase F, and evaluated with 4-12% Bis-Tris NeuPAGE and LC-MS/MS analysis of tryptic glycopeptides from modified and unmodified IgG. The molecular weights of tryptic glycopeptides helps to determine the potential site of N-linked glycosylation at each asparagine and to elucidate the species of predominant glycans.

(225) Anti-HER2 GAb201

(226) A glycoantibody derived from conventional Trastuzumab (Herceptin) bearing a glycan structure of GlcNAc-Fuc in the Fc region was treated with one or more endoglycosidases (Endo S and/or Endo F1, Endo F2, Endo F3), and then treated with an alpha-fucosidase to cleave the core fucose with a high cleavage efficiency and lead to a glycoantibody with a monosaccharide GlcNAc in the Fc region.

(227) Mixtures of Endo S (10 g), Endo F1/Endo F2/Endo F3 (10 g), Fucosidase (2 mg) and Trastuzumab (2 mg) in 50 mM sodium phosphate buffer (pH 7) were shaking at 37 C. for 24 hr. The reaction mixture was subjected to protein A affinity column for purification. The fraction of anti-HER2 GAb201 was collected (yield: 96.6%). The collected fraction was trypsinized. The trypsinized glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb201.

(228) Anti-HER2 GAb101

(229) Ethanol was added into 100 mL of chicken egg yolk and mixed thoroughly. After centrifugation, the supernatant was discarded and the pellet was collected. The pellet was washed twice with ethanol. Water was added into the pellet and mixed thoroughly. The mixture was centrifuged. After centrifugation, the supernatant was discarded and the pellet was collected. The pellet was mixed with ethanol. A supernatant was collected and lyophilized to obtain 1.5 g white de-fat powder. The powder was dissolved in phosphate buffer and treated with 1 mg endo--N-acetylglucosaminidase for enzymatic digestion. The reaction mixture was mixed with water-soluble organic solvent thoroughly and centrifuged to collect the supernatant The supernatant was purified by ion exchange column. 18 mg of glycan-101 (Sia.sub.2Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc) was obtained.

(230) A solution of glycan-101 (Sia.sub.2(2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column eluted by 0.05% aqueous Et.sub.3N to collect the glycan oxazoline-101.

(231) Glycan oxazoline-101 was added to a mixture of endoglycosidase and anti-HER2 GAb201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb101. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb101.

(232) Anti-HER2 GAb102

(233) A solution of glycan-102 (Sia (2-6)Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-102) were combined and lyophilized to give a white powder.

(234) Glycan oxazoline-102 was added to a mixture of endoglycosidase and anti-HER2 GAb201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb02. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb102.

(235) Anti-HER2 GAb103

(236) A solution of glycan-103 (Sia(2-6)GalGlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water (593 L) was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-103) were combined and lyophilized to give a white powder.

(237) Glycan oxazoline-103 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb103. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb103.

(238) Anti-HER2 GAb104

(239) A solution of glycan-104 (Gal.sub.2GlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-104) were combined and lyophilized to give a white powder.

(240) Glycan oxazoline-104 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb104. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb104.

(241) Anti-HER2 GAb 105

(242) A solution of glycan-105 (GalGlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-105) were combined and lyophilized to give a white powder.

(243) Glycan oxazoline-105 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb105. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb 105.

(244) Anti-HER2 GAb 106

(245) A solution of glycan-106 (GalGlcNAcMan.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water (593 L) was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex 0-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-106) were combined and lyophilized to give a white powder.

(246) Glycan oxazoline-106 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb106. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb106.

(247) Anti-HER2 GAb107

(248) A solution of glycan-107 (GlcNAc.sub.3Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-107) were combined and lyophilized to give a white powder.

(249) Glycan oxazoline-107 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb107. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb107.

(250) Anti-HER2 GAb 108

(251) A solution of glycan-108 (GlcNAc.sub.2Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-108) were combined and lyophilized to give a white powder.

(252) Glycan oxazoline-108 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb108. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb 108.

(253) Anti-HER2 GAb109

(254) A solution of glycan-109 (GlcNAcMan.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-109) were combined and lyophilized to give a white powder.

(255) Glycan oxazoline-109 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb109. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb109.

(256) Anti-HER2 GAb110

(257) A solution of glycan-110 (GlcNAcMan.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-110) were combined and lyophilized to give a white powder.

(258) Glycan oxazoline-110 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb110. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb110.

(259) Anti-HER2 GAb111

(260) A solution of gycan-111 (Man.sub.3GlcNAc) (30 mg), 2-chloro-1,3-dimethylimidazolinium chloride (DMC) (62.7 mg) and Et.sub.3N (89 L) in water was stirred at 4 C. for 1 h. The reaction mixture was subjected to gel filtration chromatography on a Sephadex G-25 column and eluted by 0.05% aqueous Et.sub.3N. The fractions containing the product (glycan oxazoline-111) were combined and lyophilized to give a white powder.

(261) Glycan oxazoline-111 was added to a mixture of endoglycosidase and anti-HER2 GAb 201 in 50 mM Tris buffer (pH 7.8) and incubated for an hour at room temperature. The reaction mixture was purified with protein A affinity column, followed by amanion exchange column capto Q to collect the desired product, anti-HER2 GAb111. The product was trypsinized, and the glycopeptides, TKPREEQYNSTYR (SEQ ID NO: 3) and EEQYNSTYR (SEQ ID NO: 4), were analyzed using nanospray LC/MS to confirm the glycosylation pattern of anti-HER2 GAb111.

Example 2: Characterization of Anti-HER2 GAbs

(262) General

(263) MS spectrometry analysis of of glycoengineered mAb. Intact molecular weights of glycoengineered antibodies were detected by LC-ESI-MS on a LTQ Orbitrap XL ETD mass spectrometer (Thermo Fisher Scientific, San Jose, Calif.) equipped with ACQUITY UPLC (Waters, Milford, Mass.), using a BEH C4 column (1.0 mm150 mm, 1.7 m, Waters, Milford, Mass.). Briefly, the gradient employed was 1% buffer B at 3 min to 40% buffer B at 20 min with a flow rate of 50 uL/min, where buffer A was 0.1% formic acid in H.sub.2O and buffer B was 0.1% formic acid in 80% acetonitrile. Full-scan MS condition: mass range m/z 800-4000 with Iontrap. Electrospray voltage was maintained at 4.0 kV and capillary temperature was set at 275 C.

(264) For the analysis of trypsinized glycopeptides, high resolution and high mass accuracy nanoflow LC-MS/MS experiments were done on a LTQFT Ultra (Linear quadrupole ion trap Fourier transform ion cyclotron resonance) mass spectrometer (Thermo Electron, san Jose, Calif.) equipped with a nanoelectrospry ion source (New Objective, Inc.), an Agilent 1100 Series binary high-performance liquid chromatography pump (Agilent Technologies, Palo Alto, Calif.), and a Famos autosampler (LC Packings, San Francisco, Calif.). The digestion solution was injected (6 l) at 10 l/min flow rate on to a self packed precolumn (150 m I.D.20 mm, 5 m. 100 ). Chromatographic separation was performed on a self packed reversed phase C18 nano-column (75 m I.D.300 mm, 5 m, 100 ) using 0.1% formic acid in water as mobile phase A and 0.1% formic acid in 80% acetonitrile as mobile phase B operated at 300 nl/min flow rate. Survey full-scan MS condition: mass range m/z 320-2000, resolution 100,000 at m/z 400. The ten most intense ions were sequentially isolated for MS2 by LTQ. Electrospray voltage was maintained at 1.8 kV and capillary temperature was set at 200 C.

(265) Analysis of N-Glycosylation in Trastuzumab

(266) We developed a mass spectrometric method to monitor the yield of oligosaccharide-derived fragment ions (oxonium ions) over a collision induced dissociation (CID) energy applied to a glycopeptides precursor. Multiple Reaction Monitoring (MRM) of oxonium ions method could fulfill the regulatory requirement on the routine quality control analysis of forthcoming biosimilar therapeutics.

(267) 5 g of Trastuzumab was dissolved in 25 L of 2M Guanidine-HCl, and dithiothreitol (DTT) were added to a final concentration of 5 mM. After 10 minutes incubation in 110 C., reduced cysteine residues were alkylated in 10 mM lodoacetamide (IAA) at 37 C. for 1 hour. Add 5 mM DTT to quench excess IAA at RT for 10 minutes. The product was diluted 15 times in 50 mM ammonium bicarbonate before microcentrifugation with spin column (10 kDa protein MW cut-off). The trypsin digestion was performed for 4 hours at 37 C. using an enzyme: protein ratio of 1:25 (w/w). Sample was frozen at 20 C. for LC-MS/MS analysis.

(268) The glycopeptide quantification by m/z 204 oxonium ion (HexNAc) monitoring was performed using a 4000 QTrap triple quadrupole mass spectrometer (AB Sciex) with Aglient 1200 HPLC system. For relative quantification of glycopeptide microheterogeneity, precursor ion m/z was derived in-silico, covering all possible glycan compositions, and a single quantitative transition was monitored for each precursor ion (Q3 m/z=204).

(269) MS Data Analysis

(270) The acquired raw data was processed with Analyst 1.5 (AB Sciex). The mass chromatogram of each transition was integrated and quantified by peak area. The percentage composition of each component was calculated with respect to the sum of all components combined.

(271) Glycan oxazoline-101 was added to mixture of EndoS and anti-HER2 GAb201 in 50 mM Tris buffer (pH7.8) and incubated for 0.5-1 hr at r.t. or 30 C. After the reaction is completed, anti-HER2 GAb101 was purified with protein A affinity column and loaded to an anion exchange column capto Q for further purification. The purified anti-HER2 GAb101 was confirmed by SDS-PAGE, and the molecular weight of the IgG molecule of anti-HER2 GAb101 was confirmed by MS (Table 6, FIGS. 3 and 4 for anti-HER2 GAbs 101 and 104). The N-glycan profiling was performed by trypsin digestion, and analyzed by nanospray LC/MS based on the cleavaged glycopeptide TKPREEQYNSTYR (SEQ ID NO: 3). Anti-HER2 GAbs 102, 104, 105, 106, 107, 108, 110 and 111 were synthesized in the same manner, and analyzed by the same procedures as described herein. Results of N-glycan profiling for anti-HER2 GAbs 101, 102, 104, 105, 106, 107, 108, 110 and 111 are shown in Table 7. FIGS. 5 and 6 show the MS of the cleavaged glycopeptide TKPREEQYNSTYR (SEQ ID NO: 3) after trypsin digestion of anti-HER2 GAbs 101 and 104.

(272) Table 6. ESI/MS Analysis: Intact Molecular Weight of Anti-HER2 Gabs

(273) TABLE-US-00005 TABLE 6 Anti-HER2 Glycan Theroy Delta Ms GAb Apex Delta Mass DeltaMass/2 Composition Mass (Da) 200 145652.650453 0 0 110 147443.710616 1791.06 895.5301 +N2H3 893.32 2.2101 105 148181.406009 2528.756 1264.378 +N3H4 1258.45 5.928 106 148175.984898 2523.334 1261.667 +N3H4 1258.45 3.217 111 147037.808231 1385.158 692.5789 +N1H3 690.24 2.3389 102 148760.418231 3107.768 1553.884 +N3H4S1 1549.55 4.334 108 147843.822838 2191.172 1095.586 +N3H3 1096.40 0.814 107 148258.908231 2606.258 1303.129 +N4H3 1299.48 3.649 104 148500.403787 2847.753 1423.877 +N3H5 1420.51 3.367 101 149665.698231 4013.048 2006.524 +N3H5S2 2002.70 3.824

(274) N-glycan profiling of anti-HER2 Gabs is shown in FIG. 19.

Example 3: Anti-Her2 GAb ELISA Binding Assay

(275) General

(276) SDS-PAGE detection of glycoengineered Herceptin antibodies. All the SDS-PAGE analysis was performed with NuPAGE Novex 4-12% Bis-Tris gel (Invitrogen) ether with or without DTT addition.

(277) Recombinant human HER2 protein (purchased from Sino Biological Inc.) (1 g/mL) in 100 L carbonate coating buffer (pH 10) was coated onto 96 well high binding plates at 4 C. for overnight. 2% of bovine serum albumin in PBST was then added to block plates at r.t. for 1 hr and subsequently a series dilution of anti-HER2 GAbs 101, 102, 104, 105, 106, 107, 108, 110 and 111 were added to plates and incubated for one hour. After incubation, HRP conjugated anti-human IgG was added to the reaction mixture and incubated for one hour. An aliquot of OPD substrate was added, and the absorbance at 450 nm was recorded. Throughout the experiment, plates were washed with PBS twice after each incubation step. Results of ELISA binding are shown in FIG. 20.

Example 4: ADCC Reporter Bioassay of Anti-HER2 GAbs in SK-BR-3 Cells

(278) ADCC assay was performed with Promega reporter bioassay kit. Target cell, SK-BR-3 cancer cell line was obtained from ATCC and maintained in McCoy's 5A (modified) medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum and 1% Antibiotic-Antimycotic (Gibco). When ready for ADCC assay, SK-BR-3 cells were harvested and plated in 384 well microplates for 2 days. Then, series tritration of Herceptin with different glycan forms were added and followed by incubation with NFAT engineered Jurkat cells expressing FcIIIa receptor with V158 variant for 6 hrs at 37 C. The readout was done through adding Bio-Glow luciferase substrate to plates and recorded with victor3 luminescence plate reader. The ratio of effector cell to target cell is 12.5. Results are shown in FIG. 7 and Table 9.

(279) TABLE-US-00006 TABLE 9 lists ADCC activities of anti-HER2 GAbs and Trastuzumab. Anti-HER2 Trastuzumab GAb101 GAb104 GAb105 GAb107 GAb108 GAb111 ADCC 1 30 14.3 9.5 10 6.5 3 (fold)

Example 5: Binding Affinity of Anti-HER2 GAbs to FcRIIIA

(280) General

(281) Surface Plasmon Resonance (SPR) Analysis.

(282) All the SPR experiments were performed with BIACORE T200 at 25 C. using HBS-EP (10 mM HEPES pH7.4, 0.15M NaCl, 3mMEDTA, 0.005% surfactant P20) as running buffer. The (Fab).sub.2 fragment of goat anti-human (Fab).sub.2 (Jackson Immuno Research Inc.) was utilized to capture antibody samples after immobilized onto both the reference and active channels of CM5 sensor chip. Interactions between glycoengineered antibodies and complex-type glycosylated FcRIIIA (expressed from HEK293 cells) were recorded through single cycle kinetic methods using five different concentrations of FcRIIIA at 30 ul/min for association with 240 seconds followed by dissociation time of 420 seconds. Data was processed with double-referencing for background subtraction and fitted to 1:1 Langmuir binding model in BiaEvaluation software (GE Healthcare) to get kinetic/affinity constants.

(283) FcRIIIA was transfected into HEK-293 cell line to express recombinant protein. The secreted FcRIIIA recombinant protein was purified and then diluted to serial concentration in HBS-EP buffer (200 nM, 100 nM, 50 nM, 25 nM, and 12.5 nM). Each of anti-HER2 GAb101, GAb102, GAb103, GAb104, GAb105, GAb106, GAb107, GAb108, GAb109, GAb 10 and GAb111 was diluted in HBS-EP buffer to the concentration of 10 mg/ml, and then captured to the CM5 chip in which anti-human Fab domain antibodies were pre-immobilized. A serial titration of FcRIIIA was injected and bound at the flow rate of 30 ml/min. Single cycle kinetics data was fitted into 1:1 binding model using Biacore T200 evaluation software to measure the equilibrium constant (Ka/Kd). The results were shown in Table 4.