Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6854—Immunoglobulins
  • G01N33/6857—Antibody fragments
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
  • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
  • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
  • A61K47/56—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
  • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
  • A61K47/60—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K19/00—Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/40—Immunoglobulins specific features characterized by post-translational modification
  • C07K2317/41—Glycosylation, sialylation, or fucosylation
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
  • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
  • C07K2317/622—Single chain antibody (scFv)
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide

Definitions

• the present invention relates generally to single-chain antigen-binding molecules capable of glycosylation. More specifically, the invention relates to antigen-binding proteins having Asn-linked glycosylation sites capable of attaching a carbohydrate moiety. The invention also relates to multivalent antigen-binding molecules capable of glycosylation. The invention further relates to glycosylated antigen-binding molecules capable of polyalkylene oxide conjugation.
• compositions of, genetic constructions for, methods of use, and methods for producing glycosylated antigen-binding proteins capable of polyalkylene oxide conjugation are disclosed.
• the invention also relates to methods for producing a polypeptide having increased glycosylation and the polypeptide produced by the described methods.
• Antibodies are proteins generated by the immune system to provide a specific molecule capable of complexing with an invading molecule, termed an antigen. Natural antibodies have two identical antigen-binding sites, both of which are specific to a particular antigen. The antibody molecule "recognizes" the antigen by complexing its antigen-binding sites with areas of the antigen termed epitopes. The epitopes fit into the conformational architecture of the antigen- binding sites of the antibody, enabling the antibody to bind to the antigen.
• the IgG antibody e.g., is composed of two identical heavy and two identical light polypeptide chains, held together by interchain disulfide bonds. The remainder of this discussion on antibodies will refer only to one pair of light/heavy chains, as each light/heavy pair is identical.
• Each individual light and heavy chain folds into regions of approximately 110 amino acids, assuming a conserved three- dimensional conformation.
• the light chain comprises one variable region (V L ) and one constant region (C L ), while the heavy chain comprises one variable region (V H ) and three constant regions (C H 1, C H 2 and C H 3). Pairs of regions associate to form discrete structures. In particular, the light and heavy chain variable regions associate to form an "Fv" area which contains the antigen-binding site.
• a multivalent antigen-binding protein has more than one antigen-binding site.
• a multivalent antigen-binding protein comprises two or more single-chain protein molecules. Enhanced binding activity, di- and multi-specific binding, and other novel uses of multivalent antigen-binding proteins have been demonstrated. See, Whitlow, M., et al, Protein Engng. 7:1017-1026 (1994); Hoogenboom,
• Carbohydrate modifications of proteins fall into three general categories: ⁇ -linked (or Asn-linked) modification of asparagine, O-linked modification of serine or threonine and glycosyl-phosphatidylinositol derivation of the C-terminus carboxyl group.
• ⁇ -linked (or Asn-linked) modification of asparagine O-linked modification of serine or threonine
• glycosyl-phosphatidylinositol derivation of the C-terminus carboxyl group Each of these transformations is catalyzed by one or more enzymes which demonstrate different peptide sequence requirements and reaction specificities.
• ⁇ -linked glycosylation is catalyzed by a single enzyme, oligosaccharyl transferase (OT), and involves the co-translational transfer of a lipid-linked tetradecasaccharide (Glc ⁇ Ac 2 -Man 9 -Glc 3 ) to an asparagine side chain within a nascent polypeptide (see, Imperiali, B. and Hendrickson, T.L.,
• the asparagine residue must reside within the tripeptide ⁇ -linked glycosylation consensus sequence Asn-Xaa- Thr/Ser ( ⁇ XT/S), where Xaa can be any of the 20 natural amino acids except proline.
• ⁇ XT/S tripeptide ⁇ -linked glycosylation consensus sequence Asn-Xaa- Thr/Ser
• Xaa can be any of the 20 natural amino acids except proline.
• a natural ⁇ -linked glycosylation sequence (Asn-Val-Thr) at amino acid positions 18-20 was identified in the framework- 1 (FR-1) region of the light chain variable domain of a murine anti-B cell lymphoma antibody, LL-2 (Leung, S.-o. et al, J Immunol. 154:5919-5926 (1995)).
• Hydrazides readily form relatively stable hydrazone linkages by condensation with aldehydes and ketones (Andresz, H. et al, Makromol Chem. 779:301 (1978)). This property has been used extensively for modification of glycoproteins through oxidized oligosaccharide moieties (Wilchek, M. & Bayer, E.A., Meth. Enzymol. 138:429 (1987)).
• Activated PEG-hydrazide allows it to react with an aldehyde group.
• Aldehyde is normally absent on the polypeptide chain of a protein.
• carbohydrate can be activated to provide a reactive aldehyde group by oxidation of the sugar ring such as mannose.
• Methods for activation of immunoconjugates are described in Sela et al, Immunoconjugates, Vogel ed., Oxford University Press (1987). In this way, PEG-hydrazide can be conjugated covalently to the protein via the carbohydrate structure.
• Zalipsky, S., et al, WO 92/16555 describes PAO covalently bonded to an oxidized carbohydrate moiety of the glycopolypeptide by a linkage containing a hydrazide or hydrazone functional group bound to the polymer.
• the oxidation of the carbohydrate moiety produces reactive aldehydes.
• the hydrazone linkage is formed by reacting an acyl hydrazine derivative of the polymer containing the peptide sequence with these aldehyde groups.
• Zalipsky inU.S. PatentNo. 5,122,614, disclosed poly(ethylene glycol)-N- succinimide carbonate and its preparation. This form of the polymer was said to react readily with the amino groups of proteins, as well as low molecular weight peptides and other materials that contain free amino groups.
• linkages between the amino groups of the protein, and the PEG are also known in the art, such as urethane linkages (Veronese et al, Appl. Biochem. Biotechnol 77:141-152 (1985)), carbamate linkages (Beauchamp et al, Analyt.
• polyalkylene oxide modification of sFvs is disclosed in U.S. Provisional Patent Application No. 60/050,472, filed June 23, 1997, which disclosure is incorporated herein by reference.
• the activated polymers can also be reacted with a therapeutic agent having nucleophilic functional groups that serve as attachment sites.
• nucleophilic functional group commonly used as an attachment site is the e-amino groups of lysines.
• Free carboxylic acid groups, suitably activated carbonyl groups, oxidized carbohydrate moieties and mercapto groups have also been used as attachment sites.
• the invention is directed to a single-chain antigen-binding polypeptide capable of glycosylation, comprising: (a) a first polypeptide comprising the antigen binding portion of the variable region of an antibody heavy or light chain;
• the single-chain antigen-binding polypeptide has at least one tripeptide Nsn-linked glycosylation sequence comprising Nsn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, wherein the tripeptide glycosylation sequence is capable of attaching a carbohydrate moiety at the Asn residue located at a position selected from the group consisting of (i) the amino acid position 11, 12, 13, 14 or 15 of the light chain variable region; (ii) the amino acid position 77, 78 or 79 of the light chain variable region; (iii) the amino acid position 11, 12, 13, 14 or 15 of the heavy chain variable region; (iv) the amino acid position
• a peptide linker linking the first and second polypeptides (a) and (b) into a single chain polypeptide having an antigen binding site, wherein the single-chain antigen-binding polypeptide has at least one tripeptide Asn-linked glycosylation sequence comprising Asn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, wherein the tripeptide glycosylation sequence is capable of attaching a carbohydrate moiety at the Asn residue located at a position selected from the group consisting of (i) the amino acid position 11, 12, 13, 14 or 15 of the light chain variable region; (ii) the amino acid position 77, 78 or 79 of the light chain variable region; (iii) the amino acid position 11, 12, 13, 14 or 15 of the heavy chain variable region; (iv) the amino acid position 82B, 82C or 83 of the heavy chain variable region; (v) any amino acid position of the peptide linker
• the invention is directed to a replicable cloning or expression vehicle comprising the above described DNA sequence.
• the invention is also directed to such vehicle which is a plasmid.
• the invention is further directed to a host cell transformed with the above described DNA.
• the host cell may be a bacterial cell, a yeast cell or other fungal cell, an insect cell or a mammalian cell line.
• a preferred host is Pichia pastor is.
• the invention is directed to a method of producing a single-chain antigen- binding polypeptide capable of glycosylation, comprising:
• the host cell is capable of catalyzing glycosylation.
• the host cell is a plant cell, a bacterial cell, a yeast cell or other fungal cell, an insect cell or a mammalian cell line.
• N preferred host cell is Pichia pastoris.
• the invention is further directed to a multivalent single-chain antigen- binding protein, comprising two or more single-chain antigen-binding polypeptides.
• each single-chain antigen-binding polypeptide comprising: (a) a first polypeptide comprising the antigen binding portion of the variable region of an antibody heavy or light chain;
• a peptide linker linking the first and second polypeptides (a) and (b) into a single chain polypeptide having an antigen binding site, wherein the single-chain antigen-binding polypeptide has at least one tripeptide Asn-linked glycosylation sequence comprising Asn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, wherein the tripeptide glycosylation sequence is capable of attaching a carbohydrate moiety at the Asn residue located at a position selected from the group consisting of (i) the amino acid position 11, 12, 13, 14 or 15 ofthe light chain variable region; (ii) the amino acid position 77, 78 or 79 ofthe light chain variable region; (iii) the amino acid position 11, 12, 13, 14 or 15 of the heavy chain variable region; (iv) the amino acid position 82B, 82C or 83 ofthe heavy chain variable region; (v) any amino acid position ofthe peptide linker
• the tripeptide glycosylation sequence may be capable of attaching a carbohydrate moiety at the Asn residue located at a position selected from the group consisting of (i') the amino acid position 12 of the light chain variable region; (ii') the amino acid position 77 ofthe light chain variable region; (iii') the amino acid position 13 of the heavy chain variable region; (iv') the amino acid position 82B of the heavy chain variable region; (v 1 ) the amino acid position 2 of the peptide linker; (vi') adjacent to the C-terminus ofthe second polypeptide (b); and (vii') combinations thereof, wherein the glycosylated single-chain antigen-binding polypeptide is capable of binding an antigen.
• At least one single-chain antigen-binding polypeptide may have at least two tripeptide glycosylation sequences in tandem such that the Asn residues are separated by two amino acid residues and/or at least one set of two overlapping tripeptide glycosylation sequences such that the Asn residues are adjacent.
• At least one single-chain antigen-binding polypeptide may have three tripeptide glycosylation sequences in tandem.
• At least one single-chain antigen-binding polypeptide may have at least two sets of two tandem tripeptide glycosylation sequences and at least two sets of two overlapping tripeptide glycosylation sequences.
• the Asn residue ofthe tripeptide glycosylation sequence may be attached to a carbohydrate moiety.
• the carbohydrate moiety may further be conjugated to polyalkylene oxide.
• the carbohydrate and/or polyalkylene moieties may be conjugated to one or plurality of peptide, lipid, nucleic acid, drug, toxin, chelator, boron addend or detectable label molecule(s).
• the carbohydrate and/or polyalkylene oxide moieties may be conjugated to a carrier having one or plurality of peptide, lipid, nucleic acid, drug, toxin, chelator, boron addend or detectable label molecule(s) bound to the carrier.
• the C-terminus of the second polypeptide (b) may be the native C-terminus of the second polypeptide (b).
• the C-terminus ofthe second polypeptide (b) may comprise a deletion of one or plurality of amino acid residue(s), such that the remaining N-terminus amino acid residues ofthe second polypeptide are sufficient for the glycosylated polypeptide to be capable of binding an antigen.
• the C-terminus ofthe second polypeptide may comprise an addition of one or plurality of amino acid residue(s), such that the glycosylated polypeptide is capable of binding an antigen.
• the Asn residue of the glycosylation sequence may be located adjacent to any ofthe above mentioned
• C-terminus of the second polypeptide and the glycosylation sequence may be followed by at least one amino acid residue.
• the glycosylation sequence may be followed by two, three, four or five amino acid residues.
• the first polypeptide (a) may comprise the antigen binding portion of the variable region of an antibody light chain and the second polypeptide (b) comprises the antigen binding portion ofthe variable region of an antibody heavy chain.
• the invention is also directed to a method of detecting an antigen suspected of being in a sample, comprising: (a) contacting the sample with the glycosylated polypeptide or multivalent protein of the invention, wherein the carbohydrate moiety is conjugated to one or plurality of detectable label molecule(s), or conjugated to a carrier having one or plurality of detectable label molecule(s) bound to the carrier; and (b) detecting whether the glycosylated single-chain antigen-binding polypeptide has bound to the antigen.
• the invention is further directed to a method of imaging the internal structure of an animal, comprising administering to the animal an effective amount of the glycosylated polypeptide or multivalent protein ofthe invention, wherein the carbohydrate moiety is conjugated to one or plurality of detectable label or chelator molecule(s), or conjugated to a carrier having one or plurality of detectable label or chelator molecule(s) bound to the carrier, and measuring detectable radiation associated with the animal.
• Animal includes human and nonhuman.
• the invention is also directed to a method for treating a targeted disease, comprising administering an effective amount of a composition comprising the glycosylated polypeptide or multivalent protein of the invention and a pharmaceutically acceptable carrier vehicle, wherein the carbohydrate moiety is conjugated to one or plurality of peptide, lipid, nucleic acid, drug, toxin, boron addend or radioisotope molecule(s), or conjugated to a carrier having one or plurality of drug, toxin, boron addend or radioisotope molecule(s) bound to the carrier.
• glycosylated polypeptide or multivalent protein of the invention which is conjugated to polyalkylene oxide which may also be conjugated to one or plurality of peptide, lipid, nucleic acid, drug, toxin, chelator, boron addend or detectable label molecule(s).
• the invention also relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa- Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the tripeptide glycosylation sequences are in tandem such that the Asn residues are separated by two amino acid residues; and (b) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced by the described process.
• the invention further relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least one set of two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the two tripeptide glycosylation sequences overlap such that the Asn residues are adjacent; and (b) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced by the described process.
• the invention also relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa- Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the tripeptide glycosylation sequences are in tandem such that the Asn residues are separated by two amino acid residues; (b) providing to the polynucleotide at least one set of two tripeptide Asn-linked glycosylation sequences, wherein the two tripeptide glycosylation sequences overlap such that the Asn residues are adjacent; and (c) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced
• FIG. 1 DNA sequence and translated protein sequences of CC49/218 SCA with engineered N-linked glycosylation sites indicated.
• the variable light (V L ) and variable heavy (V H ) chains are indicated. Restriction sites are underlined and named.
• CDR sequences are double underlined.
• the 218 linker is underlined and named.
• Proposed tripeptide N-linked glycosylation sites are underlined.
• the mutations made to generate the N-linked glycosylation sites are shown in parenthesis underneath the proposed glycosylation sites and the site of oligosaccharide attachment is denoted under the mutated sequence by * and numbered.
• the C-terminal extension for glycosylation is shown in parenthesis.
• FIG. 1 Binding of serial dilutions of parent CC49/218 SCA obtained from E. coli GX9251 (A) or P. pastoris ⁇ N225 (B) to immobilized bovine submaxillary mucin in ELISA.
• the purified CC49/218 SCA from E. coli (100 ⁇ g/ml) and the unpurified culture supernatant from P. pastoris EN225 (-50 ⁇ g/ml SCA) were assayed for direct binding of antigen as described in Materials and Methods.
• Absorbance at 405 nm (A405) was measured after 10 min of PNPP substrate incubation with the alkaline phosphatase conjugated rabbit anti-mouse antibody. Two controls are shown at the right. Cl records the absorbance of
• C2 shows the background binding of induced P. pastoris host GS1 15 (3.3-fold dilution) to immobilized bovine submaxillary mucin.
• FIG. 3 Western blot analysis of CC49/218 SCA and glyco-SCA before and after enzymatic treatment with N-acetylglucosamine specific endoglycosidases.
• Unpurified CC49/218 SCA from culture supematants of EN225, EN235 and EN236 were digested with Peptide-N-glycosidase F or Endo- glycosidase H.
• the samples ( ⁇ 1 ⁇ g per lane) were run on a 4-20% SDS-PAGE slab gel and transferred to a nitrocellulose membrane for Western analysis using a rabbit anti-CC49/218 SCA polyclonal antibody.
• the Coomassie Blue stained gel was scanned using a Molecular Dynamics Laser Scanner Model PD-SI and the area quantitation is displayed for the purified sample (A) and the starting supernatant (B).
• the ratios of glycosylated SCA (peak 1) to unmodified SCA (peak 2) are 1.2 (A) and 1.1 (B).
• 1 and 2 correspond to bands 1 and 2, respectively.
• Figure 6 Kabat consensus V K I/218/V H III SCA with engineered glycosylation sites. Amino acid sequence and engineered N-linked glycosylation sites for a consensus human SCA protein containing a V L domain (derived from a human kappa light chain subgroup I consensus sequence) and a V H domain
• Proposed tripeptide N-linked glycosylation sites are underlined and the site of oligosaccharide attachment is indicated by * .
• Proposed residue(s) change to generate N-linked glycosylation site is in parenthesis below.
• the C-terminal extension for glycosylation is shown in parenthesis.
• the three uncommon V K I CDR1 positions 27D, 27E, and 27F are not shown.
• the V H III terminal position 113 is optional and alternate SCA may terminate at position 112.
• Proline residues flanking the tripeptide sequence in the +3 position are changed to alanines, as recommended by the compilation of Gavel, Y., and von Heijne, G., Protein Engng. 5:433-442 (1990).
• FIG. 7 C6.5/218 SCA with engineered glycosylation sites.
• Amino acid assignments ofthe wild-type C6.5 variable domains are according to Schier, R., et al, J. Mol. Biol 255:28-43 (1996).
• CDR sequences are double underlined.
• the 218 linker is overlined and named.
• Proposed tripeptide N-linked glycosylation sites are underlined and the site of oligosaccharide attachment is indicated by * .
• Proposed residue(s) change to generate N-linked glycosylation site is in parenthesis below.
• the C-terminal extension for glycosylation is shown in parenthesis.
• the V H terminal position 113 is optional and an alternate SCA may terminate at position 112.
• Proline residues flanking the tripeptide sequence in the +3 position are changed to alanines, as recommended by the compilation of Gavel, Y., and von Heijne, G., Protein Engng. 5:433-442 (1990).
• Figure8 A33/218 SCA with engineered glycosylation sites.
• Amino acid assignments conform to the numbering system of Kabat et al. , Sequences of Proteins of Immunological Interest, 5th ed., U.S. Dept. Health and Human Services, Bethesda, MD (1991). CDR sequences are double underlined. The 218 linker is overlined and named.
• Proposed tripeptide N-linked glycosylation sites are underlined and the site of oligosaccharide attachment is indicated by *.
• Proposed residue(s) change to generate N-linked glycosylation site is in parenthesis below. The C-terminal extension for glycosylation is shown in parenthesis.
• Figure 9 Western blot analysis of CC49/218 SCA and glyco-CC49/218 SCA, having one, two, or three glycosylation sites, before and after treatment with Endo-glycosidase H. Conditions were as described above. Lane 1, control P. pastoris host GSl 15; Lane 2, CC49/218 SCA; Lanes 3 and 4, glyco-CC49/218 SCA EN236 (one glycosylation site); Lanes 5 and 6, glyco-CC49/218 SCA EN279 (two glycosylation sites); Lanes 7 and 8, glyco-CC49/218 SCA EN280 (three glycosylation sites). Lanes 4, 6, and 8, treated with Endo-glycosidase H.
• CC49 SCA E. coli CC49 and P. pastoris ⁇ N 225
• GS 115 R. pastoris host
• -*— BS A
• ⁇ - E. coli CC49
• -*- GSl 15
• - - ⁇ N225
• -g- EN236;
• FIG. 11 A. SEC chromatography of glycosylated and PEG- modified CC49 with two tandem glycosylation sites.
• the glyco-CC49/2 (EN279) was purified by a combination of cation exchange chromatography and anion exchange chromatography.
• Conditions for PEGylation (PEG modification) ofthe glycosylated CC49/2 were as described in Example 4.
• SEC chromatography of the reaction mixture showed the appearance of high molecular weight peaks in addition to the low molecular weight non-glycosylated peak which was the only peak before PEGylation.
• B. SDS-PAGE analysis ofthe reaction mixture showed that the glycosylated and PEGylated CC49/2 was all converted to a higher molecular weight species (lane 2).
• Lanes 2 and 3 contained a 50/50 mixture of glycosylated and non-glycosylated CC49 which was not PEG hydrazide modified.
• the non-glycosylated CC49/2 (Lane 3) remained at the position corresponding to the un-modified species. This indicated that the reaction was specific for the carbohydrate moiety and did not affect the SCA that contains no carbohydrate.
• Lanes 1 and 4 contained molecular weight standards.
• FIG. 12 SDS-PAGE analysis of the fractions from size exclusion chromatography after PEGylation of glyco-CC49/2 (EN279).
• Lane 1 molecular weight marker
• Lane 2 native unPEGylated gCC49/2 (nonglycosylated and glycosylated fractions)
• Lane 3, low molecular weight fraction Lane 4, high molecular weight fraction (PEGylated and glycosylated single chain gCC49/2).
• FIG. 13 SDS-PAGE analysis of gCC49/3 (glyco-CC49/triple sites) (EN280) and PEGylated gCC49/3. Conditions for PEGylation ofthe glycosylated CC49/3 were as described in Example 5. Lane 1, native un-PEGylated glycosylated CC49/3; Lane 2, gCC49/3-HZ5,000-PEG (highly PEGylated fraction); Lane 3, gCC49/3-HZ5,000-PEG (less PEGylated fraction); Lane 4, molecular weight marker (116.3, 97.4, 66.3, 55.4, 36.5, 31, 26.5 (CC29/218- native), 21.5, 14.4, 6 kDa). Both the highly PEGylated and less PEGylated fractions ofthe PEGylated and glycosylated CC49/3 had molecular weights much higher than that ofthe un-PEGylated glycosylated CC49/3.
• the invention relates to the discovery that glycosylated single-chain antigen-binding molecules ("SCA") or single-chain variable fragments of antibodies (“sFv”) have significant utility beyond that of the nonglycosylated single-chain antigen-binding proteins.
• SCA glycosylated single-chain antigen-binding molecules
• sFv single-chain variable fragments of antibodies
• a glycosylated SCA protein has a carbohydrate moiety which acts as a second biological effector.
• the oligosaccharide functions may include cellular and tissue targeting, specific binding and interactions with serum proteins, specific binding and interactions with cell receptors, cell matrix and intracellular proteins.
• the invention is directed to monovalent and multivalent SCA proteins capable of glycosylation, compositions of monovalent and multivalent glycosylated SCA proteins, methods of making and purifying monovalent and multivalent glycosylated SCA proteins, and uses for glycosylated SCA proteins.
• the invention is also directed to glycosylated SCA proteins having a diagnostic or therapeutic agent covalently attached to an Asn-linked carbohydrate moiety.
• single-chain antigen-binding molecule SCA
• single-chain Fv single-chain Fv
• SCA single-chain antigen-binding molecule
• sFv single-chain Fv
• They are structurally defined as comprising the binding portion of a first polypeptide from the variable region of an antibody V L (or V H ), associated with the binding portion of a second polypeptide from the variable region of an antibody V H (or V L ), the two polypeptides being joined by a peptide linker linking the first and second polypeptides into a single polypeptide chain, such that the first polypeptide is N- terminal to the linker and second polypeptide is C-terminal to the first polypeptide and linker.
• the single polypeptide chain thus comprises a pair of variable regions connected by a polypeptide linker.
• the regions may associate to form a functional antigen-binding site, as in the case wherein the regions comprise a light-chain and a heavy-chain variable region pair with appropriately paired complementarity determining regions (CDRs).
• CDRs complementarity determining regions
• the single-chain protein is referred to as a "single-chain antigen-binding protein" or "single-chain antigen-binding molecule.”
• V L is the N-terminal domain followed by the linker and V H (a V L -Linker-V H construction) or V H is the N-terminal domain followed by the linker and V L (V H - Linker- V L construction) .
• the preferred embodiment contains V L in the N-terminal domain (see, Anand, N.N., et al, J. Biol. Chem. 266:2 ⁇ 874-21879 (1991)).
• multiple linkers have also been used.
• Several types of sFv proteins have been successfully constructed and purified, and have shown binding affinities and specificities similar to the antibodies from which they were derived.
• the Fv domains have been selected from the group of monoclonal antibodies known by their abbreviations in the literature as 26-10, MOPC 315, 741F8, 520C9, McPC 603, D1.3, murine phOx, human phOx, RFL3.8 sTCR, 1 A6, Sel55-4, 18-2-3, 4-4-20, 7A4-1 , B6.2, CC49, 3C2, 2c, MA- 15C5/K 12 G 0 , Ox, etc. (see, Huston, J.S. et al, Proc. Natl Acad. Sci. USA 55:5879-5883 (1988); Huston, J.S. et al, SIM News 38(4) (Supp.f.U (1988);
• Linkers ofthe invention used to construct SCA polypeptides are designed to span the C-terminus of V L (or neighboring site thereof) and the N-terminus of V H (or neighboring site thereof) or between the C-terminus of V H and the N-terminus of V L .
• the preferred length ofthe peptide linker should be from 2 to about 50 amino acids. In each particular case, the preferred length will depend upon the nature of the polypeptides to be linked and the desired activity of the linked fusion polypeptide resulting from the linkage. Generally, the linker should be long enough to allow the resulting linked fusion polypeptide to properly fold into a conformation providing the desired biological activity. Where conformational information is available, as is the case with SCA polypeptides discussed below, the appropriate linker length may be estimated by consideration of the 3-dimensional conformation ofthe substituent polypeptides and the desired conformation ofthe resulting linked fusion polypeptide.
• linker length may be empirically determined by testing a series of linked fusion polypeptides with linkers of varying lengths for the desired biological activity. Such linkers are described in detail in WO 94/12520, which disclosure is incorporated herein by reference.
• Preferred linkers used to construct SCA polypeptides have between 10 and 30 amino acid residues.
• the linkers are designed to be flexible, and it is recommended that an underlying sequence of alternating Gly and Ser residues be used.
• three charged residues may be included, two positively charged lysine residues (K) and one negatively charged glutamic acid residue (E).
• K positively charged lysine residues
• E negatively charged glutamic acid residue
• one ofthe lysine residues is placed close to the N-terminus of V H , to replace the positive charge lost when forming the peptide bond ofthe linker and the V H .
• linker lengths of equal to or greater than
• linkers having 18 to 30 residues are most preferred for SCA polypeptides in the monovalent conformation. Linker lengths of less than 10 residues are favored for SCA in the multimer conformation.
• Another property that is important in engineering an SCA polypeptide, or any other linked fusion polypeptide, is proteolytic stability.
• the 212 linker (Pantoliano et al. , Biochemistry 30: 101 17 ( 1991 )) is susceptible to proteolysis by subtilisin BPN'.
• the proteolytic clip in the 212 linker occurs between Lys8 and Ser9 ofthe linker (see Table 1). By placing a proline at the proteolytic clip site one may be able to protect the linker.
• Table 1 shows various linkers for illustration. See also, Whitlow, M., et al, Protein Engng. 7:1017-1026 (1994).
• the 217 linker contains a lysine- proline pair at positions 6 and 7; the 218 linker contains the lysine-proline pair at positions 8 and 9, respectively, thus rendering the linker less susceptible to proteolysis.
• the 218 linker demonstrates less aggregation, greater proteolytic stability , and the necessary flexibility and solubility to result in a functional linker for SCA proteins.
• a second guiding consideration in linker design is that a linker with reduced aggregation is preferable.
• the 18-residue 216 linker shows reduced aggregation as compared to the 14-residue 212 linker.
• the first eleven residues of the 216 linker are identical to the 212 linker, including the proteolytically-susceptible peptide bond between Lys8 and Ser9. Thus, it is believed that the extra four residues contribute to the lowered aggregation. Linkers with 18 or more residues are thus most preferred.
• a linker was designed in which a proline was substituted for serine at position 9, after Lys8, in the 18-residue 216 linker.
• the linker is designated 218 (see Table 1). See WO 94/12520, which disclosure is incorporated herein by reference.
• Positioning the proline at the proper place in the linker sequence to inhibit proteolysis is accomplished by determining the points of proteolytic attack in the susceptible sequence.
• a protease such as subtilisin BPN' is contacted with the candidate linker. Cleavage can then be determined by sequencing the resulting peptides, which will also reveal the cleavage point or points, if any. Any protease may be used, and selection will be guided by consideration ofthe environment the linker is to encounter in actual use.
• the requirements for an SCA is that the linker be longer than 12 amino acids.
• the preferred length ofthe linker in an SCA is greater than 18 residues, in order to reduce aggregation, as described above.
• multivalent SCAs For multivalent SCAs, the association of two or more SCAs is required for their formation.
• multivalent SCAs can be produced from SCAs with linkers as long as 25 residues, they tend to be unstable. Holliger, P., et al, Proc. Natl Acad. Sci. USA 90:6444-6448 (1993), have recently demonstrated that linkers 0 to 15 residues in length facilitate the formation of divalent Fvs. See, Whitlow, M., et al, Protein Engng. 7:1017-1026 (1994); Hoogenboom, H.R., Nature Biotech. 75:125-126 (1997); and WO 93/11161.
• the object of the present invention is to produce an SCA having one or more (or at least one) Asn-linked glycosylation sequence(s) such that the Asn- linked glycosylation site (the asparagine residue within the glycosylation sequence) is capable of attaching a carbohydrate moiety and the glycosylated polypeptide is capable of binding an antigen (i.e., the glycosylated polypeptide's ability to bind an antigen is not disrupted).
• the SCA may have one, two, three, five, seven or ten N-linked glycosylation sequence(s), but not limited to the numbers recited.
• Asn-linked glycosylation also referred to as N-linked glycosylation, occurs when sugar residues are linked through the amide nitrogen of asparagine residues. Intracellular biosynthesis of Asn-linked oligosaccharides occurs in both the lumen ofthe endoplasmic reticulum and following transport of the protein to the Golgi apparatus. Asn-linked glycosylation occurs at the following tripeptide glycosylation consensus sequence: Asn-Xaa-Yaa (Asn-Xaa- Thr/Ser; NXT/S), where Xaa may be any amino acid except proline and Yaa is serine or threonine.
• All Asn-linked oligosaccharides have a common pentasaccharide core (Man 3 GlcNAc 2 ) originating from a common biosynthetic intermediate. They differ in the number of branches and the presence of peripheral sugars such as fucose and sialic acid. They can be categorized according to their branched constituents, which may consist of mannose only (high mannose N-glycans); alternating GlcNAc and Gal residues terminated by various sugar sequences, and with the possibility of intrachain substitutions of bisecting Fuc and core GlcNAc (complex
• a further object ofthe invention is to produce monovalent and multivalent SCAs having one or more Asn-linked glycosylation sequence(s) .
• multivalent SCAs may be generated by chemically crosslinking two SCAs with C-terminal cysteine residues (Cumber etal, J. Immunol. 149:120-126 ( 1992)) and by linking two SCAs with a third polypeptide linker to form a dimeric Fv (George et al. J. Cell. Biochem. 15 E: ⁇ 21 (1991)). Details for producing multivalent SCAs by aggregation are described in Whitlow, M., et al, Protein Engng. 7:1017-1026 (1994). Multivalent antigen-binding fusion proteins ofthe invention can be made by any process, but preferably according to the process for making multivalent antigen-binding proteins set forth in WO 93/11161, which disclosure is incorporated herein by reference.
• Yet a further object of the invention is to produce monovalent or multivalent SCAs, as described above, having at least two tripeptide glycosylation sequences in tandem such that the Asn residues are separated by two amino acid residues.
• Another object ofthe invention is to produce monovalent or multivalent SCAs, as described above, having at least one set of two overlapping tripeptide glycosylation sequences such that the Asn residues are adjacent.
• Another object ofthe invention is to produce monovalent or multivalent glycosylated SCAs, as described above, which are conjugated to polyalkylene oxide.
• N-linked glycosylation sites within the tripeptide glycosylation consensus sequences may occur in the V L and V H regions, the C-terminus ofthe second polypeptide (V L , V H or neighboring site thereof), the N-terminus ofthe first polypeptide (V L , V H or neighboring site thereof), the linker region between the first and second polypeptide regions, or occur in a combination of these regions.
• the design of the carbohydrates site on a protein involves examining the structural information known about the protein and the residues in the proteins involved in antigen binding. The carbohydrates sites are chosen to be as far from these residues as possible so as to prevent disruption ofthe antigen- binding site. See Hubbard, S.C, and Ivatt, R.i., Ann. Rev. Biochem. 50:555-583 (1981), for review of synthesis and processing of Asn-linked glycosylation.
• the glycosylation sequence may occur adjacent to the (1) native C-terminus residue of V L (or V H ), (2) the C-terminus of V L (or V H ) wherein the C-terminus has a deletion of one or plurality of amino acid residue(s), such that the remaining N-terminus amino acid residues ofthe peptide are sufficient for the glycosylated polypeptide to be capable of binding an antigen, or (3) the
• C-terminus of V L wherein the C-terminus residue has an addition of one or plurality of amino acid residue(s), such that the glycosylated polypeptide is capable of binding an antigen.
• native is intended the naturally occurring C- terminus ofthe immunoglobulin (second polypeptide).
• C-terminus it is well understood in the art as intending the C-terminus amino acid residue or the
• C-terminus region of a polypeptide which could include up to all ofthe amino acid residues ofthe polypeptide excluding the first N-terminus amino acid residue ofthe polypeptide.
• C-terminus is intended as the C-terminus amino acid residue of the above-mentioned three types of C-terminus (1, 2 or 3), unless otherwise indicated or intended.
• Glycosylation sequences were identified and engineered at residues within loop sites in regions of the SCA that are diametrically opposed to the antigen binding site.
• the five loop regions and C-terminal extension chosen as preferred sites of glycosylation are among the most distant regions spatially removed from the binding site.
• the six furthest portions of an SCA from the antigen binding site are as follows: 1) The loop made up of residues 11 to 15 in the light chain;
• the nucleic and amino acid sequences of each loop are examined for possible N-linked glycosylation sequences which may be engineered into the loop region.
• the best sites are those in which it takes a minimum number of amino acid changes to generate the Asn-Xaa-Thr/Ser glycosylation sequence.
• Thr occurs in successfully glycosylated tripeptide sequences about two times as often as Ser.
• sequence homology rules such as the "GeneWorks" Program from Intelligenetics, Inc. (Mountain View, CA).
• the engineered placement ofthe N ofthe N-X-S/T sequence anywhere in these six identified regions can generate a preferred site for SCA glycosylation.
• Figure 1 shows the following resulting designs: designed glycosylation sites no. 1 and no. 2 in the light chain of the CC49/218 SCA; designed glycosylation site no. 3 in the N-terminal end of the linker in CC49/218 SCA; designed glycosylation sites no. 4 and no. 5 in the heavy chain ofthe CC49/218 SCA; designed glycosylation site no. 6 adjacent to the C-terminus of the CC49/218 SCA. Any combination of these six sites could be used.
• the design approach can be used for other SCAs, such as a Kabat consensus V /218/V H III, C6.5/218 and A33/218, as shown in Figures 6-8, respectively.
• nucleotide sequence which is used to introduce an Asn- linked glycosylation sequence into the various positions will depend upon the naturally-occurring nucleotide sequence.
• the most preferred sites are those in which it takes a minimum number of amino acid changes to generate the Asn- linked glycosylation sequence.
• glycosylation sequence no. 1 in Figure 1 was generated by mutating amino acid 12, Pro (CCT), to Asn (AAC), resulting in an Asn-linked glycosylation sequence of Asn-Val-Ser.
• CCT Pro
• AAC Asn
• other Asn-linked sequences may be generated.
• a particular amino acid may be encoded by multiple nucleotide sequences.
• Site-directed mutagenesis is used to change the native protein sequence to one that incorporates the designed sites of N-linked glycosylation.
• the mutant protein gene is placed in an expression system that is capable of glycosylating the protein, such as bacterial cells, yeast or other fungal cells, insect cells or mammalian cells. It may be important to find a system that uniformly glycosylates the mutant glycoprotein.
• the mutant glycoprotein can be purified by standard purification methods. Oligonucleotide-directed mutagenesis methods for generating the Asn- linked glycosylation sequences and related techniques for mutagenesis of cloned DNA are well known in the art. See, Sambrook et al.
• MOLECULAR CLONING A LABORATORY MANUAL, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989); Ausubel etal (eds.), CURRENT PROTOCOLS IN MOLECULAR
• Example 1 Materials and Methods section, infra.
• a single chain antigen binding molecule e.g., CC49
• the genetic sequence polynucleotide
• a single chain antigen binding molecule with the genetic sequence (polynucleotide) available for glycosylation can be made to contain the carbohydrate moiety by a post-translation process that is available in eukaryotic cells, such as in the yeast Pichia.
• the gCC49 was derived from the original clone CC49/218 by incorporating glycosylation genetic sequences. Several clones were created.
• Plasmid pEN270 was transformed into Pichia to give a clone EN279 that secretes glycosylated CC49-protein designated as gCC49/2. This clone contained two glycosylation sequences. The gene product produced by the yeast had over
• Plasmid pEN271 was transformed into Pichia to give a clone EN280 that secretes glycosylated CC49 protein designated as gCC49/3.
• This clone contained three glycosylation sequences.
• the gene product produced by the yeast had over 90%) ofthe single chain antigen-binding protein in the glycosylated form.
• CC49 having exemplary one, two or three glycosylation sequence(s) (in bold) adjacent to the C-terminus are provided below.
• CC49 with one glycosylation sequence adjacent to the C-terminus includes the glycosylation sequence N-K-77 (amino acids depicted in bold are those necessary for a glycosylation site).
• CC49 with two tandem glycosylation sequences adjacent to the C-terminus is also shown: N-K-T-N-A-T. Additionally,
• the SCA may have two or more (or at least two), such as three, five, seven, or ten, for example, ⁇ -linked glycosylation sequences in tandem, or one or more (or at least one) set, such as three, five, seven, or ten, for example, sets of two tandem sequences.
• the SCA may have one or more (or at least one) set, such as two, three, five, seven or ten, for example, sets of two overlapping sequences.
• the glycosylated CC49 was purified by a combination of cation exchange chromatography and anion exchange chromatography.
• the protein fraction that contains no carbohydrate was removed by size exclusion chromatography.
• proteins may also be modified by the addition of tandem or overlapping glycosylation sequences.
• Such proteins include, but are not limited to, disulfide-stabilized Fv fragments (Reiter, Y. et al, Nature Biotech. 14:1239- 1245 (1996)), camel immunoglobulins (Muyldermans, S. et al, Protein Engng. 7:1129-1135 (1994)), cancer vaccines, cell adhesion proteins such as selectin, members ofthe immunoglobulin superfamily including IgG, IgM, IgE, IgD and IgA as well as other immunoglobulin family proteins.
• therapeutic enzymes such as DNase, RNase, and catabolic enzymes, cytokines, hormones, and growth factors such as erythropoietin, GCSF (Granulocyte colony stimulating factor), GMCSF (Granulocyte macrophage colony stimulating factor).
• cytokines such as erythropoietin
• GCSF Granulocyte colony stimulating factor
• GMCSF GMCSF
• interleukin-2 alpha-interferon
• insulin human growth hormone
• other blood proteins such as tissue plasminogen activator and Factor VIII and Factor XI.
• these methods may be applied to vaccines such as hepatitis
• B vaccine B vaccine, AIDS vaccines, lyme disease vaccines, and other infectious disease vaccines.
• Use of this technology also includes the selective N-linked modification of gene therapy vectors including viral vectors, non-viral vectors, and cellular vectors which contain such engineered N-linked glycoproteins. It is surprising that SCA containing multiple tandem and/or overlapping glycosylation sequences are more completely glycosylated than an SCA containing a single glycosylation sequence as carbohydrate attachment at Asn residues near or adjacent to each other would be expected to encounter steric hindrance. Specifically, the two-sequence version was greater than 50%o modified and the three-sequence version was greater than 95%) modified compared to the single-site version which was about 35-50%) modified.
• the invention relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the tripeptide glycosylation sequences are in tandem such that the Asn residues are separated by two amino acid residues; and (b) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced by the described process.
• the invention further relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least one set of two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa-Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the two tripeptide glycosylation sequences overlap such that the Asn residues are adjacent; and (b) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced by the described process.
• the invention also relates to (1) a method of producing a polypeptide having increased glycosylation, comprising: (a) providing to a polynucleotide encoding the polypeptide at least two tripeptide Asn-linked glycosylation sequences, wherein each tripeptide glycosylation sequence comprises Asn-Xaa- Yaa, wherein Xaa is an amino acid other than proline and Yaa is threonine or serine, and wherein the tripeptide glycosylation sequences are in tandem such that the Asn residues are separated by two amino acid residues; (b) providing to the polynucleotide at least one set of two tripeptide Asn-linked glycosylation sequences, wherein the two tripeptide glycosylation sequences overlap such that the Asn residues are adjacent; and (c) expressing the polynucleotide in a host cell capable of attaching a carbohydrate moiety at the Asn residues, and (2) a polypeptide having increased glycosylation produced
• polynucleotide is intended DNA, RNA or a genetic sequence. After mutating the nucleotide sequence ofthe SCA, the mutated DNA can be inserted into a cloning vector for further analysis, such as for confirmation of the DNA sequence.
• the DNA sequence is operably linked to regulatory sequences controlling transcriptional expression and introduced into either a prokaryotic or eukaryotic host cell.
• SCAs are typically produced by prokaryotic host cells
• eukaryotic host cells are the preferred host cells.
• Preferred host cells include plant cells, yeast or other fungal cells, insect cells or mammalian cells. Standard protein purification methods may be used to purify these mutant glycoproteins.
• DNA molecules such as purified genetic sequences or plasmids or vectors encoding the SCA of the invention that have engineered sequences capable of N-linked glycosylation.
• the DNA sequence for the glycosylated SCA polypeptide can be chosen so as to optimize production in organisms such as plant cells, prokaryotes, yeast or other fungal cells, insect cells or mammalian cells.
• the DNA molecule encoding an SCA having Asn-linked glycosylation sequences can be operably linked into an expression vector and introduced into a host cell to enable the expression ofthe glycosylated SCA protein by that cell.
• a DNA sequence encoding an SCA having Asn-linked glycosylation sequences may be recombined with vector DNA in accordance with conventional techniques.
• procaryotic hosts include, but are not limited to, bacteria such as Neisseria, Mycobacteria, Streptococci, Chlamydia and E. coli which expresses recombinant heterologous enzymes capable of glycosylation.
• Eukaryotic hosts for cloning and expression of such SCA proteins ofthe invention include insect cells, yeast, fungi, and mammalian cells (such as, for example, human or primate cells) either in vivo, or in tissue culture.
• a preferred host for the invention is Pichia pastoris.
• the appropriate DNA molecules, hosts, methods of production, isolation and purification of monovalent, multivalent and fusion forms of proteins, especially SCA polypeptides, are thoroughly described in the prior art, such as, e.g., U.S. Patent No. 4,946,778, which disclosure is incorporated herein by reference.
• the SCA encoding sequence having Asn-linked glycosylation sequences and an operably linked promoter may be introduced into a recipient prokaryotic or eukaryotic cell either as a non-replicating DNA (or RNA) molecule, which may either be a linear molecule or, more preferably, a closed covalent circular molecule. Since such molecules are incapable of autonomous replication, the expression ofthe desired SCA protein may occur through the transient expression of the introduced sequence. Alternatively, permanent expression may occur through the integration of the introduced SCA sequence into the host chromosome. In one embodiment, the SCA sequence can be integrated into the host cell chromosome.
• Cells which have stably integrated the introduced DNA into their chromosomes can be selected by also introducing one or more markers which allow for selection of host cells which contain the SCA sequence and marker.
• the marker may complement an auxotrophy in the host (such as his4, leu2, or ura3, which are common yeast auxotrophic markers), biocide resistance, e.g., antibiotics, or resistance to heavy metals, such as copper, or the like.
• the selectable marker gene can either be directly linked to the SCA DNA sequence to be expressed, or introduced into the same cell by co-transfection.
• the introduced sequence will be incorporated into a plasmid vector capable of autonomous replication in the recipient host cell.
• a plasmid vector capable of autonomous replication in the recipient host cell.
• Any of a wide variety of vectors may be employed for this purpose. Factors of importance in selecting a particular plasmid or viral vector include: the ease with which recipient cells that contain the vector may be recognized and selected from those recipient cells which do not contain the vector; the number of copies ofthe vector which are desired in a particular host; and whether it is desirable to be able to "shuttle" the vector between host cells of different species.
• yeast vector systems Any of a series of yeast vector systems can be utilized. Examples of such expression vectors include the yeast 2-micron circle, the expression plasmids YEP13, YCP and YRP, etc., or their derivatives. Such plasmids are well known in the art (Botstein et al, Miami Wntr. Symp. 19:265-214 (1982); Broach, J.R., In: The Molecular Biology of the Yeast Saccharomyces: Life Cycle and Inheritance, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p. 445- 470 (1981); Broach, J.R., Cell 25:203-204 (1982)). For a mammalian host, several possible vector systems are available for expression.
• vectors utilize DNA elements which provide autonomously replicating extra-chromosomal plasmids, derived from animal viruses such as bovine papilloma virus, polyoma virus, adenovirus, or SV40 virus.
• a second class of vectors relies upon the integration ofthe desired gene sequences into the host chromosome. Cells which have stably integrated the introduced
• DNA into their chromosomes may be selected by also introducing one or more markers which allow selection of host cells which contain the expression vector.
• the marker may provide for prototropy to an auxotrophic host, biocide resistance, e.g., antibiotics, or resistance to heavy metals, such as copper or the like.
• the selectable marker gene can either be directly linked to the DNA sequences to be expressed, or introduced into the same cell by co-transformation. Additional elements may also be needed for optimal synthesis of mRNA. These elements may include splice signals, as well as transcription promoters, enhancers, and termination signals.
• the cDNA expression vectors incorporating such elements include those described by Okayama, H., Mol. Cell. Biol. 5:280 (1983), and others.
• vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from Qiagen; pBS vectors, Phagescript vectors, Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available from Stratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia.
• preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXTl and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia.
• Preferred vectors for expression in Pichia are pHIL-S 1 (Invitrogen Corp.) and pPIC9 (Invitrogen Corp.). Other suitable vectors will be readily apparent to the skilled artisan.
• the DNA constructs may be introduced or transformed into an appropriate host.
• Various techniques may be employed, such as transformation, transfection, protoplast fusion, calcium phosphate precipitation, electroporation, or other conventional techniques.
• the cells After the cells have been transformed with the recombinant DNA (or RNA) molecule, the cells are grown in media and screened for appropriate activities. Expression of the sequence results in the production ofthe glycosylated SCA ofthe present invention.
• N-linked glycosylation can be achieved in vitro by reacting the mutant SCA polypeptides described herein with purified N-linked glycosylation enzymes and further reacting such glycosylated SCA with other carbohydrate modifying enzymes.
• the straight chain polyalkylene glycols employed in the practice ofthe present invention are ofthe structural formula
• R is selected from the group consisting of hydrogen, lower alkyl, and mixtures thereof
• R 1 is selected from the group consisting of hydrogen and lower alkyl
• n is a positive integer.
• lower alkyl is meant an alkyl group having from one to four carbon atoms, i.e., methyl, ethyl, propyl, butyl, and isomers of the foregoing.
• R is preferably selected from the group consisting of hydrogen, methyl, and mixtures thereof
• R 1 is preferably selected from the group consisting of hydrogen and methyl
• n is preferably a positive integer of 500 or less.
• R is most preferably hydrogen
• R 1 is most preferably methyl
• n is most preferably an integer of 7 to 150.
• poly(alkylene glycols) employed in the practice ofthe present invention are poly(ethylene glycol), poly(propylene glycol), mixtures thereof, and copolymers of poly(ethylene glycol) and poly (propylene glycol), wherein one of the terminal hydroxyl groups ofthe polymer may be substituted with a lower alkyl group.
• a preferred polyalkylene glycol for use in the present invention is poly(ethylene glycol)-hydrazide.
• the polyalkylene glycol employed in the practice ofthe present invention will be designated PAG, which term is intended to include both compounds wherein R 1 is hydrogen and compounds wherein R 1 is alkyl.
• PEG refers to poly(ethylene glycol) and mPEG refers to methoxy poly(ethylene glycol).
• the PAG does not have to be of a particular molecular weight, but it is preferred that the molecular weight be between about 500 and about 40,000; more preferably, between about 2,000 and about 20,000.
• the choice of molecular weight of PAG is made based on the nature of the particular polypeptide employed, for example, the number of amino or other groups available on the polypeptide for modification. Molecular weights of about 10,000 and about
• the terminal hydroxyl groups of PEG can be transformed into amine, carboxyl, or hexamethyl isocyanate groups. See, for example, Zalipsky et al, 1983, supra.
• a mixed anhydride derivative of carboxylated mPEG can be prepared in the presence of triethylamine and then reacted with proteins:
• Carboxylated mPEG can also be reacted with hydroxysuccinimide in the presence of dicyclohexylcarbodiimide and dimethyl formamide for reaction with protein:
• BSC-PEG polyethylene glycol-bis-succinidyl carbonate
• activated PAGs can also be employed in the practice ofthe present invention.
• the preferred activated PAG for use in the practice ofthe present invention is PEG-hydrazide.
• the invention further provides for the use of branched, substantially non- antigenic polymers for PEGylation of the SCA proteins corresponding to the formula:
• (n) 2 or 3;
• (L) is an aliphatic linking moiety covalently linked to each (R); and
• (A) represents an activated functional group capable of undergoing nucleophilic substitution.
• (A) can be a group which is capable of bonding with biologically active nucleophiles or moieties capable of doing the same.
• R includes a poly(alkylene oxide) PAO such as poly(ethylene glycol) PEG or mPEG. It is preferred that each chain have a molecular weight of between about 200 and about 12,000 daltons and preferably between about 1,000 and about 10,000 daltons. Molecular weights of about 5,000 daltons are most preferred.
• PAO poly(alkylene oxide) PAO
• PAO poly(ethylene glycol) PEG or mPEG. It is preferred that each chain have a molecular weight of between about 200 and about 12,000 daltons and preferably between about 1,000 and about 10,000 daltons. Molecular weights of about 5,000 daltons are most preferred.
• 2 or 3 polymer chains are j oined to the aliphatic linking moiety (L) .
• Suitable aliphatics included substituted alkyl diamines and triamines, lysine esters and malonic ester derivatives.
• the linking moieties are preferably non-planar, so that the polymer chains are not rigidly fixed.
• the linking moiety (L) is also a means for attaching the multiple polymer chains or "branches" to (A), the moiety through which the polymer attaches to the SCA protein.
• (L) preferably includes a multiply-functionalized alkyl group containing up to 18, and more preferably between 1-10 carbon atoms.
• a heteroatom such as nitrogen, oxygen or sulfur may be included within the alkyl chain.
• the alkyl chain may also be branched at a carbon or nitrogen atom.
• (L) is a single nitrogen atom.
• (L) and (R) are preferably joined by a reaction between nucleophilic functional groups on both (R) and (L). Each (R) is suitably functionalized to undergo nucleophilic substitution and bond with (L). Such functionalization of polymers is readily apparent to those of ordinary skill in the art. A wide variety of linkages are contemplated between (R) and (L).
• Urethane (carbamate) linkages are preferred.
• the bond can be formed, for example, by reacting an amino group such as l,3-diamino-2-propanol with methoxypoly ethylene glycol succinimidyl carbonate as described in U.S. Patent No. 5,122,614.
• Amide linkages which can be formed by reacting an amino- terminated non-antigenic polymer such as methoxypoly ethylene glycol-amine (mPEG amine) with an acyl chloride functional group. Examples of other such linkages include ether, amine, urea, and thio and thiol analogs thereof, as well as the thio and thiol analogs ofthe urethane and amide linkages discussed supra.
• the moiety (A) of Formula II represents groups that "activate" the branched polymers ofthe present invention for conj ugation with biologically active materials.
• (A) can be a moiety selected from:
• Functional groups capable of reacting with an amino group such as: a) carbonates such as the p-nitrophenyl or succinimidyl; b) carbonyl imidazole; c) azlactones; d) cyclic imide thiones; or e) isocyanates or isothiocyanates.
• Functional groups capable of reacting with carboxylic acid groups and reactive with carbonyl groups such as: a) primary amines; or b) hydrazine and hydrazide functional groups such as the acyl hydrazides, carbazates, semicarbamates, thiocarbazates, etc.
• nucleophiles capable of reacting with an electrophilic center.
• a non-limiting list includes, for example, hydroxyl, amino, carboxyl, thiol groups, active methylene and the like.
• the moiety (A) can also include a spacer moiety located proximal to the aliphatic linking moiety (L).
• the spacer moiety may be a heteroalkyl, alkoxyl, alkyl containing up to 18 carbon atoms or even an additional polymer chain.
• the spacer moieties can be added using standard synthesis techniques.
• the branched polymers are formed using conventional reaction techniques known to those of ordinary skill in the art. These umbrella-like branched polymers ofthe present invention (U-P AO ' s or U-PEG's) react with biologically active nucleophiles to form conjugates. The point of polymer attachment depends upon the functional group (A).
• (A) can be a succinimidyl succinate or carbonate and react with e-amino ly sines.
• the branched polymers can also be activated to link with any primary or secondary amino group, mercapto group, carboxylic acid group, reactive carbonyl group or the like found on biologically active polypeptides. Other groups are apparent to those of ordinary skill in the art.
• branched polymers One of the main advantages of the use of the branched polymers is that the branching imparts an umbrella-like three dimensional protective covering to the materials they are conjugated with. This contrasts with the string-like structure ofthe straight chain polymers discussed, supra.
• An additional advantage of the branched polymers is that they provide the benefits associated with attaching several strands of polymers to a SCA protein or carbohydrate moiety but require substantially fewer conjugation sites.
• One or more of the activated branched polymers can be attached to a biologically active nucleophile, such as an SCA protein, by standard chemical reactions.
• a biologically active nucleophile such as an SCA protein
• (L) is an aliphatic linking moiety;
• (A 1 ) represents a linkage between (L) and the nucleophile and
• (z) is an integer > 1 representing the number of polymers conjugated to the biologically active nucleophile.
• the upper limit for (z) will be determined by the number of available nucleophilic attachment sites and the degree of polymer attachment sought by the artisan.
• the degree of conjugation can be modified by varying the reaction stoichiometry using well-known techniques. More than one polymer conjugated to the nucleophile can be obtained by reacting a stoichiometric excess ofthe activated polymer with the nucleophile.
• Activated PAO can be attached to the carbohydrate moiety using the method generally described in Sea et al, Immunoconjugates, Vogel, C. Ed., Oxford University Press, p. 189 (1987), which disclosure is incorporated herein by reference. Briefly, the glycosylated SCA is oxidized with sodium periodate which provides an aldehyde group to which the PAO can bind. This reaction is stabilized by sodium borohydride. PAO attachment to polypeptides or glycopolypeptides is also described, for example, in Zalipsky, S, et al, WO 92/16555, which disclosure is incorporated herein by reference.
• the glycosylated SCA may further be modified by conjugating a diagnostic or therapeutic agent to the carbohydrate moiety ofthe SCA.
• conjugating a diagnostic or therapeutic agent to the carbohydrate moiety ofthe SCA.
• the indirect method involves reacting an antibody (or SCA), whose carbohydrate portion has been oxidized, with a carrier polymer loaded with one or plurality of peptide, lipid, nucleic acid, drug, toxin, chelator, boron addend or detectable label molecule(s).
• the glycosylated SCA may be directly conjugated with a diagnostic or therapeutic agent.
• the general procedure is analogous to the indirect method of conjugation except that a diagnostic or therapeutic agent is directly attached to an oxidized sFv component. See Hansen et al, U.S. Patent No. 5,443,953, which disclosure is incorporated herein by reference.
• the glycosylated SCA can be attached to a derivative of the particular drug, toxin, chelator, boron addend or label to be loaded, in an activated form, preferably a carboxyl-activated derivative, prepared by conventional means, e.g., using dicyclohexylcarbodiimide (DCC) or a water soluble variant thereof, to form an intermediate adduct.
• DCC dicyclohexylcarbodiimide
• drugs and toxins which have a cytotoxic effect on tumor cells or microorganisms that may infect a human and cause a lesion, in addition to the specific illustrations given above. They are to be found in compendia of drugs and toxins, such as the Merck Index and the like. Any such drug can be loaded onto a carrier or directly onto a carbohydrate moiety of SCA by conventional means well known in the art, and illustrated by analogy to those described above.
• Chelators for radiometals or magnetic resonance enhancers are also well known in the art. Typical are derivatives of ethylenediaminetetraacetic acid
• EDTA diethylenetriaminepentaacetic acid
• DTP A diethylenetriaminepentaacetic acid
• Labels such as radioisotopes, enzymes, fluorescent compounds, electron transfer agents, and the like can also be linked to carrier or directly onto a carbohydrate moiety of SCA by conventional methods well known to the art. These labels and the SCA conjugates prepared from them can be used for immunoassays and for immunohistology, much as the SCA conjugate prepared by direct attachment of the labels to the SCA. However, the loading of the conjugates according to the present invention with a plurality of labels can increase the sensitivity of assays or histological procedures, where only low extent of binding ofthe SCA to target antigen is achieved.
• Boron addends e.g., carboranes
• carboranes when attached to single-chain antigen binding molecules and targeted to lesions, can be activated by thermal neutron irradiation and converted to radioactive atoms which decay by alpha emission to produce highly cytotoxic short-range effects.
• Carboranes can be made with carboxyl functions on pendant side chains, as is well known in the art. Loading of drugs on the carrier will depend upon the potency ofthe drug, the efficiency of SCA targeting and the efficacy ofthe conjugate once it reaches its target.
• glycosylated SCA further conjugated to polyalkylene oxide, at the carbohydrate and/or polymer moiety.
• Conjugation of poly(ethylene glycol) or poly(alkylene oxide) with small organic molecules is described in Greenwald, R. ., Exp. Opin. Ther. Patents 7:601-609 (1997), Enzon Inc., WO 95/11020, and Enzon Inc., WO 96/23794, which disclosures are all incorporated herein by reference.
• PEG ballast and the active drug are described in WO 96/23794. Uses
• glycosylated SCA One ofthe major utilities ofthe glycosylated SCA is its bifunctionality (or multifunctionality, including tri-, quadri-, etc.), in which one specificity is for one type of hapten or antigen, and the second specificity is for a second molecule or receptor.
• a glycosylated SCA molecule having two distinct binding specificities has many potential uses.
• the carbohydrate moiety may be specific for a cell-surface epitope of a target cell, such as a tumor cell or other undesirable cell.
• the antigen-binding site may be specific for a cell-surface epitope of an effector cell, such as the CD3 protein of a cytotoxic T-cell.
• the glycosylated SCA protein may guide a cytotoxic cell to a particular class of cells that are to be preferentially attacked.
• both targets, the antigen and the carbohydrate receptor can be on the same cell such that one target modulates binding specificity and the other target influences uptake or intemalization.
• Mannose-specific lectins are reported to be produced on the surface fimbria of enterobacterial species such as E. coli, Salmonella, and Pseudomonas.
• Such bacteria might be bound (extensively) to the oligosaccharides of glyco-SCA, while the SCA specificity is directed to an immune cell or otherwise promotes the microbe's clearance.
• mannose specific receptors on tumor cells could have similar application.
• the bacterial lectins are also thought to be important in cell adhesion to host and infection suggesting another application.
• Carbohydrate moieties on cell, viral or particle surfaces are major determinants of their identity. Using the SCA specificity to bind to the cell, viral or particle surfaces, and having the oligosaccharide moiety project out may give that entity a new identity for interaction with other cells, virus and proteins.
• a diagnostic or therapeutic agent is a molecule or atom which is conjugated to an antibody and useful for diagnosis and for therapy. The immunoreactivity ofthe antibody is retained. Diagnostic or therapeutic agents include drugs, toxins, chelators, boron compounds and detectable labels. See “Conjugates" section, supra, for further details.
• the diagnostic or therapeutic agent may be, but is not limited to, at least one selected from a nucleic acid, a compound, a protein, an element, a lipid, an antibody, a saccharide, an isotope, a carbohydrate, an imaging agent, a lipoprotein, a glycoprotein, an enzyme, a detectable probe, and antibody or fragment thereof, or any combination thereof, which may be detectably labeled as for labeling antibodies, as described herein.
• labels include, but are not limited to, enzymatic labels, radioisotope or radioactive compounds or elements, fluorescent compounds or metals, chemiluminescent compounds and bioluminescent compounds.
• any other known diagnostic or therapeutic agent can be used in a method ofthe present invention.
• a therapeutic agent used in the present invention may have a therapeutic effect on the target cell, the effect selected from, but not limited to, correcting a defective gene or protein, a drug action, a toxic effect, a growth stimulating effect, a growth inhibiting effect, a metabolic effect, a catabolic affect, an anabolic effect, an antiviral effect, an antibacterial effect, a hormonal effect, a neurohumoral effect, a cell differentiation stimulatory effect, a cell differentiation inhibitory effect, a neuromodulatory effect, an antineoplastic effect, an anti-tumor effect, an insulin stimulating or inhibiting effect, a bone marrow stimulating effect, a pluripotent stem cell stimulating effect, an immune system stimulating effect, and any other known therapeutic effects that may be provided by a therapeutic agent delivered to a cell via a delivery system according to the present invention.
• the SCA conjugate may be used for protection, suppression or treatment of infection or disease.
• protection from infection or disease as used herein is intended “prevention,” “suppression” or “treatment.”
• Prevention involves administration of a glycosylated SCA conjugate prior to the induction of the disease.
• suppression involves administration ofthe composition prior to the clinical appearance ofthe disease.
• Treatment involves administration ofthe protective composition after the appearance of the disease. It will be understood that in human and veterinary medicine, it is not always possible to distinguish between “preventing” and “suppressing” since the ultimate inductive event or events may be unknown, latent, or the patient is not ascertained until well after the occurrence of the event or events. Therefore, it is common to use the term “prophylaxis” as distinct from “treatment” to encompass both “preventing” and “suppressing” as defined herein.
• the term “protection,” as used herein, is meant to include “prophylaxis.”
• Such additional therapeutic agents which can further comprise a therapeutic agent or composition ofthe present invention may be selected from, but are not limited to, known and new compounds and compositions including antibiotics, steroids, cytotoxic agents, vasoactive drugs, antibodies and other therapeutic modalities.
• antibiotics used in the treatment of bacterial shock such as gentamycin, tobramycin, nafcillin, parenteral cephalosporins, etc; adrenal corticosteroids and analogs thereof, such as methyl prednisolone, mitigate the cellular injury caused by endotoxins; vasoactive drugs, such as alpha receptor blocking agent (e.g., phenoxybenzamine), beta receptor agonists (e.g., isoproterenol), and dopamine are agents suitable for treating septic shock.
• alpha receptor blocking agent e.g., phenoxybenzamine
• beta receptor agonists e.g., isoproterenol
• dopamine are agents suitable for treating septic shock.
• Glycosylated SCA of the invention may also be used for diagnosis of disease and to monitor therapeutic response.
• Other uses of glycosylated SCA proteins are specific targeting of pro-drug activating enzymes to tumor cells by a bispecific molecule with specificity for tumor cells and enzyme.
• SCA may be used for specific delivery of drug to an in vivo target, such as a tumor, delivery of radioactive metals for tumor radioimmunodiagnosis or radioimmunotherapy (Goldenberg, D.M., Am. J. Med. 94:291 (1993)), nonradioactive metals in applications such as with boron/uranium-neutron capture therapy (Ranadive, G.N., et al, Nucl Med. Biol. 20: 1 (1993); Barth, R.F., et al,
• Biosensors generate a detectable signal upon binding of a specific antigen to an antigen-binding molecule, with subsequent processing ofthe signal.
• Glycosylated SCA proteins when used as the antigen-binding molecule in biosensors, may change conformation upon binding, thus generating a signal that may be detected.
• the invention is also directed to a method of detecting an antigen suspected of being in a sample by contacting the sample with the glycosylated
• a sample may comprise at least one compound, mixture, surface, solution, emulsion, suspension, mixture, cell culture, fermentation culture, cell, tissue, secretion and/or derivative or extract thereof.
• samples can also include, e.g., animal tissues, such as blood, lymph, cerebrospinal fluid (CNS), bone marrow, gastrointestinal contents, and portions, cells or internal and external secretions of skin, heart, lung and respiratory system, liver, spleen, kidney, pancreas, gall bladder, gastrointestinal tract, smooth, skeletal or cardiac muscle, circulatory system, reproductive organs, auditory system, the autonomic and central nervous system, and extracts or cell cultures thereof.
• CNS cerebrospinal fluid
• Such samples can be measured using methods ofthe present invention in vitro, in vivo and in situ.
• Such samples can also include environmental samples such as earth, air or water samples, as well as industrial or commercial samples such as compounds, mixtures, surfaces, aqueous chemical solutions, emulsions, suspensions or mixtures.
• samples that can be used in methods ofthe present invention include cell culture and fermentation media used for growth of prokaryotic or eukaryotic cells and/or tissues, such as bacteria, yeast, mammalian cells, plant cells and insect cells.
• prokaryotic or eukaryotic cells and/or tissues such as bacteria, yeast, mammalian cells, plant cells and insect cells.
• glycosylated SCA proteins of the present invention include detectably-labeled forms of the glycosylated SCA protein.
• Types of labels are well-known to those of ordinary skill in the art. They include radiolabeling, chemiluminescent labeling, fluorochromic labeling, and chromophoric labeling.
• Other uses include imaging the internal structure of an animal (including a human) by administering an effective amount of a labeled form ofthe glycosylated SCA protein and measuring detectable radiation associated with the animal. They also include improved immunoassays, including sandwich immunoassay, competitive immunoassay, and other immunoassays wherein the labeled antibody can be replaced by the glycosylated SCA protein of this invention. See, e.g., Kohler et al, Nature 256:495 (1975); Kohler etal, Eur. J. Immunol. (5:511 (1976); Kohler et al, Eur. J. Immunol.
• glycosylated SCA conjugated to polyalkylene oxide especially for, for example, reduced immunogenicity and antigenicity and longer lifetimes in the blood stream.
• glycosylated SCA conjugates ofthe invention for in vivo diagnostic and therapeutic applications will be by analogous methods to conjugates of the same or similar drugs, toxins, chelators, boron adducts or detectable labels where the diagnostic or therapeutic principle is directly linked to the antibody or a loaded carrier is linked by random binding to amine or carboxyl groups on amino acid residues ofthe antibody in a non-site-specific manner.
• Conjugates ofthe present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, such as by admixture with a pharmaceutically acceptable carrier vehicle.
• compositions suitable for effective administration will contain a therapeutically effective amount ofthe immunoconjugate, either alone, or with a suitable amount of carrier vehicle.
• Controlled release preparations may be achieved by the use of polymers to complex or absorb the immunoconjugate of the present invention.
• the controlled delivery may be exercised by selecting appropriate macromolecules (for example, polyesters, polyamino acids, polyvinyl pyrrolidone, ethylene- vinylacetate, methylcellulose, carboxymethylcellulose, orprotamine sulfate).
• the rate of drug release may also be controlled by altering the concentration of such macromolecules.
• Another possible method for controlling the duration of action comprises incorporating the therapeutic agents into particles of a polymeric substance such as polyesters, polyamino acids, hydrogels, poly(lactic acid) or ethylene vinylacetate copolymers.
• microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, by the use of hydroxymethylcellulose or gelatin-microcapsules or poly (methylmethacrylate) microcapsules, respectively, or in a colloid drug delivery system, for example, liposomes, albumin microspheres, microemulsions, nanoparticles, nanocapsules, or in macroemulsions.
• a colloid drug delivery system for example, liposomes, albumin microspheres, microemulsions, nanoparticles, nanocapsules, or in macroemulsions.
• the immunoconjugate may be provided to a patient by means well known in the art.
• Such means of introduction include oral means, intranasal means, subcutaneous means, intramuscular means, intravenous means, intra-arterial means, or parenteral means.
• Intravenous, intraarterial or intrapleural administration is normally used for lung, breast, and leukemic tumors.
• Intraperitoneal administration is advised for ovarian tumors.
• Intrathecal administration is advised for brain tumors and leukemia.
• Subcutaneous administration is advised for Hodgkin's disease, lymphoma and breast carcinoma.
• Catheter perfusion is useful for metastatic lung, breast or germ cell carcinomas of the liver.
• Intralesional administration is useful for lung and breast lesions.
• compositions according to the invention may be administered parenterally in combination with conventional injectable liquid carriers such as sterile pyrogen-free water, sterile peroxide-free ethyl oleate, dehydrated alcohol, or propylene glycol.
• conventional injectable liquid carriers such as sterile pyrogen-free water, sterile peroxide-free ethyl oleate, dehydrated alcohol, or propylene glycol.
• Conventional pharmaceutical adjuvants for injection solution such as stabilizing agent, solubilizing agents and buffers, such as ethanol, complex forming agents such as ethylene diamine tetraacetic acid, tartrate and citrate buffers, and high-molecular weight polymers such as polyethylene oxide for viscosity regulation may be added.
• Such compositions may be injected intramuscularly, intraperitoneally, or intravenously.
• carriers and diluents include albumin and/or other plasma protein components such as low density lipoproteins, high density lipoproteins and the lipids with which these serum proteins are associated.
• These lipids include phosphatidyl choline, phosphatidyl serine, phosphatidyl ethanolamine and neutral lipids such as triglycerides.
• Lipid carriers also include, without limitation, tocopherol.
• At least one glycosylated SCA linked to a therapeutic agent according to the invention may be administered by any means that achieve their intended purpose, for example, to treat various pathologies, such as cell inflammatory, allergy, tissue damage or other related pathologies.
• a typical regimen for preventing, suppressing, or treating various pathologies comprises administration of an effective amount of an SCA conjugate, administered over a period of one or several days, up to and including between one week and about 24 months. It is understood that the dosage ofthe present invention administered in vivo or in vitro will be dependent upon the age, sex, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature ofthe effect desired.
• the ranges of effective doses provided below are not intended to limit the invention and represent preferred dose ranges. However, the most preferred dosage will be tailored to the individual subject, as is understood and determinable by one of skill in the art, without undue experimentation.
• Effective amounts of a diagnostic/pharmaceutical compound or composition of the present invention are from about 0.001 ⁇ g to about 100 mg/kg body weight, administered at intervals of 4-72 hours, for a period of 2 hours to 5 years, or any range or value therein, such as 0.01-1.0, 1.0- 10, 10-50 and 50- 100 mg/kg, at intervals of 1 -4, 6- 12, 12-24 and 24-72 hours, for a period of 0.5, 1.0-2.0, 2.0-4.0 and 4.0-7.0 days, or 1, 1-2, 2-4, 4-52 or more weeks, or 1, 2, 3-10, 10-20, 20-60 or more years, or any range or value therein.
• Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions, which may contain auxiliary agents or excipients which are known in the art.
• Pharmaceutical compositions such as tablets and capsules can also be prepared according to routine methods. See, e.g. , Berker, supra, Goodman, supra, Avery, supra and Ebadi, supra, which disclosures are entirely inco ⁇ orated herein by reference, including all references cited therein.
• compositions comprising at least one type of SCA conjugate of the invention, or, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 types of SCA conjugates, ofthe present invention may be contained in an amount effective to achieve its intended purpose.
• a pharmaceutical composition may contain suitable pharmaceutically acceptable carriers, such as excipients, carriers and/or auxiliaries which facilitate processing ofthe active compounds into preparations which can be used pharmaceutically.
• Pharmaceutical compositions may also include suitable solutions for administration intravenously, subcutaneously, dermally, orally, mucosally or rectally, and contain from about 0.01 to 99 percent, preferably from about 20 to 75 percent of active component (i.e., the SCA) together with the excipient.
• Pharmaceutical compositions for oral administration include tablets and capsules. Compositions which can be administered rectally include suppositories. See, e.g.,
• compositions may also be formulated into orally administrable compositions containing one or more physiologically compatible carriers or excipients, and may be solid or liquid in form.
• compositions may, if desired, contain conventional ingredients such as binding agents, for example, syrups, acacia, gelatin, sorbitol, tragacanth, or polyvinylpyrrolidone; fillers, such as lactose, mannitol, starch, calcium phosphate, sorbitol, cyclodextran, or methylcellulose; lubricants such as magnesium stearate, high molecular weight polymers such as polyethylene glycols, high molecular weight fatty acids such as stearic acid or silica; disintegrants such as starch; acceptable wetting agents as, for example, sodium lauryl sulfate.
• binding agents for example, syrups, acacia, gelatin, sorbitol, tragacanth, or polyvinylpyrrolidone
• fillers such as lactose, mannitol, starch, calcium phosphate, sorbitol, cyclodextran, or methylcellulose
• the oral compositions may assume any convenient form, such as tablets, capsules, lozenges, aqueous or oily suspensions, emulsions, or dry products suitable for reconstitution with water or other liquid medium prior to use.
• the liquid oral forms may, of course, contain flavors, sweeteners, preservatives such as methyl or propyl p-hydroxybenzoates; suspending agents such as sorbitol, glucose or other sugar syrup, methyl, hydroxymethyl, or carboxymethyl celluloses or gelatin; emulsifying agents such as lecithin or sorbitan monooleate or thickening agents.
• Non-aqueous compositions may also be formulated which comprise edible oils as, for example, fish-liver or vegetable oils. These liquid compositions may conveniently be encapsulated in, for example, gelatin capsules in a unit dosage amount.
• compositions according to the present invention may also be administered, if appropriate, either topically as an aerosol or, formulated with conventional bases as a cream or ointment.
• the pharmaceutical compositions of the present invention can also be administered by incorporating the active ingredient into colloidal carriers, such as liposomes. Liposome technology is well known in the art, having been described by Allison et al, Nature 252:252-254 (1974), and Dancy et al, J. Immunol 720:1109-1113 (1978).
• the above described administration ofthe compositions also include the glycosylated SCA conjugated to polyalkylene oxide.
• the CC49 monoclonal antibody was developed by Dr. Jeffrey Schlom's group at Laboratory of Tumor Immunology and Biology, National Cancer
• the unmodified CC49/218 SCA (-27 kDa) was expressed (secreted) at high levels in recombinant Pichia (about 20-100 mg/1 depending on integrated gene copy number). All of the mutant genes described above gave detectable (though reduced) expression of secreted glyco-SCA plus unglycosylated SCA as observed by protein bands in the -27-35 kDa range. Each glycosylation event would be predicted to add -2-3 kDa of mass since Pichia is reported to add oligo- mannose chains of about 8-14 residues to the core N-Acetylglucosamines (Cregg, J.M., et al, Bio/Technol. 77:905-910 (1993). The C-terminal mutant gave the highest level of expression (secretion) and two prominent bands of -27 kDa and -30 kDa in about equal proportions. Expression of secreted glyco-SCA by the mutants is summarized in Table 2.
• the purified CC49/218 SCA from E. coli GX9251 and the unpurified culture supernatant from R. pastoris EN225 were assayed for direct binding to antigen, bovine submaxillary mucin, by ELISA.
• the parent CC49/218 SCA product from both E. coli and Pichia were shown to be active in binding bovine submaxillary mucin by ELISA. This indicates that CC49/218 SCA produced in Pichia is active.
• the C-terminal plus linker double mutant (EN236) CC49/218 SCA was run on a SDS-PAGE gel ( Figure 3).
• the upper band of the doublet was selectively stained by using the GlycoTrack Carbohydrate Kit K-050 from Oxford GlycoSystems as described by the manufacturer.
• the lower -27 kDa (unmodified) band was unstained indicating that the -30 kDa band was a glycoprotein.
• C-terminus mutant (EN235) and C-terminal plus linker double mutant (EN236) CC49/218 SCAs were digested with the glycosidase Peptide-N- glycosidase (PNGase) F or Endo-glycosidase H (Oxford Glycosystems) which will specifically cleave Asparagine-linked (N-linked) carbohydrate from the polypeptide chain.
• PNGase F or Endo-glycosidase H the samples were analyzed by SDS-PAGE which showed that the former doublets
• the C-terminus mutant CC49/218 SCA doublet proteins were bound to a bovine submaxillary mucin-Sepharose affinity column and eluted by increasing urea concentrations. As shown in Figure 4, the bound and eluted doublet appeared in equal stoichiometry as in the starting sample indicating that the glyco- SCA maintains mucin-binding specificity.
• CC49/218 SCA from EN235 culture supernatant was incubated with molar excess of Con A Sepharose resin (Pharmacia Biotech). The unbound supernatant fraction was removed, and the bound fraction was eluted with alpha-D- methylmannoside. As shown in Figure 5, the glycosylated bound fraction was -30 kDa whereas the unglycosylated unbound fraction was -27 kDa.
• CC49 SCA with one, two or three glycosylation sequences in the C-terminus are shown in Figure 9.
• Western blot analysis of CC49 SCA with one glycosylation site ( Figure 9, lanes 3 and 4) adjacent to the C-terminus shows that it is a mixture of modified (-30 kDa band) and unmodified (-27 kDa band) polypeptides.
• CC49 SCA with two glycosylation sites ( Figure 9, lanes 5 and 6) had a smaller percentage of unmodified polypeptides, a mixture of one and two glycosylation site species, and a hyperglycosylated species (-43 kDa band).
• CC49 with three glycosylation sites ( Figure 9, lanes 7 and 8) had virtually no unmodified polypeptides, a mixture of two glycosylation site species and the hyperglycosylated species.
• the SCA containing three glycosylation sequences had mainly two attached oligosaccharides or hyperglycosylated species (and virtually no unmodified protein).
• the higher molecular weight hyperglycosylated species may include both the three positions attachments and/or more extensive longer-chain oligosaccharide attachments at one or more positions of glycosylation.
• the unmodified CC49 SCA E. coli CC49 and P. pastoris ⁇ N225
• EN236 one C-terminal glycosylation sequence
• EN279 two glycosylation sequences
• EN280 three glycosylation sequences
• CC49/218 SCA was obtained from plasmid pGX5608 (Enzon, Inc.). The complete DNA sequence of CC49/218 SCA has been reported (Filpula, D., etaL, "Production of Single-chain Fv Monomers and Multimers, In:
• Pre-cast polyacrylamide slab gels (4-20%>) were obtained from Novex Corporation (San Diego, CA).
• Bovine submaxillary mucin type I, porcine submaxillary mucin type III and CNBr-activated Sepharose 4B were purchased from Sigma Inc. (St. Louis, MO).
• Con A Sepharose was obtained from Pharmacia Biotech (Piscataway, NJ).
• Purified CC49/218 SCA protein derived from E. coli GX9251 was obtained from ⁇ nzon, Inc.
• Rabbit anti- CC49/218 SCA polyclonal antibody was obtained from HRP Inc. (Denver, PA).
• Mouse anti-CC49/218 polyclonal antibody was obtained from ⁇ nzon, Inc.
• Oligonucleotide 5228 3' PCR primer for cloning two N-linked glycosylation sites at C-terminal of CC49 into BamHI site of vector PhilSl :
• Oligonucleotide 5229 3' PCR primer to put three N-linked glycosylation sites at C-terminal of CC49 into BamHI site of vector PhilSl :
• Olignucleotide 5230 3' PCR primer to put two N-linked glycosylation sites at C-terminal of CC49 into EcoRI site of vector pPic9:
• SDS-PAGE Polyacrylamide gel electrophoresis in the presence of SDS was performed using pre-cast 4-20%> slab gels from Novex Corporation (San Diego, CA) according to the manufacturer's instructions. Protein bands were visualized by staining with Coomassie Blue. Area quantitation of stained bands was performed using a Molecular Dynamics PD-SI laser scanner.
• Blot development was also performed according to the procedures in this manual. Briefly, the blotted membranes were blocked in 1%> BSA blocking reagent in PBS at room temperature for 2 hr; washed 3x with PBS; and incubated with 3%> BSA in PBS with a 1 : 1,000 dilution of rabbit anti-CC49/218 SCA antibody at 4°C overnight.
• the gel was poured into a 10 ml column and washed with 25 ml of 0.1 M Tris-HCl, pH 8.0, 0.1 M NaCl.
• the EN235 Pichia culture supernatant was dialyzed against 0.1 M Tris-HCl, pH 7.4, 0.1 M NaCl at 4°C overnight, then loaded onto the mucin- Sepharose column.
• Elution of the bound SCA proteins was performed by using 10 ml of eluent 1 (0.1 M sodium citrate, pH 4.0) followed by 10 ml of eluent 2 (8 M urea, 0.1 M Tris-HCl, pH 7.4).
• eluent 1 0.1 M sodium citrate, pH 4.0
• eluent 2 8 M urea, 0.1 M Tris-HCl, pH 7.4
• Glycoprotein staining The GlycoTrackTM carbohydrate detection kit (Cat. No.
• K-050 was purchased from Oxford GlycoSystems (Rosedale, NY) and used according to the manufacturer's instructions.
• Con A Sepharose was obtained from Pharmacia Biotech (Cat. No. 17-0440-03) and was used according to the manufacturer's instructions.
• One ml of resin in binding buffer (20 mM Tris-HCl, pH 7.4, 0.5 M NaCl) was incubated with 50 ⁇ l of dialyzed EN235 culture supernatant for 30 min at 22 °C. The beads were pelleted by microcentrifugation, and the supernatant was removed. Elution of the bound glyco-SCA was performed by washing the resin with binding buffer containing 0.2 M alpha-D- methylmannoside.
• ELISA for SCA binding activity. Immunoassay procedures were performed using modifications of protocols from Harlow, E., & Lane, D., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, (1988). Direct binding assays were performed and a dose response curve was constructed. Bovine submaxillary mucin (250 ng per 100 ⁇ l well) antigen was used to coat microtiter plate wells (MaxiSorp, Nunc, VWR Scientific, Boston, MA). The EN225 or purified CC49/218 SCA proteins were diluted serially in PBS containing 1 % BSA and incubated in the coated wells at 22°C for 1 hr.
• oligonucleotide-directed mutagenesis is employed to create Asn-linked glycosylation consensus sequences in the identified loop regions of a Kabat consensus V K I/218/V H III SCA, C6.5/218 SCA, and A33/218 SCA, as shown in Figures 6-8, respectively (i.e., (1) two V L changes; (2) two V H changes; (3) one linker change; (4) one C-terminal change; or (5) combinations thereof).
• V K I/218/V H III SCA and C6.5/218 SCA proline residues flanking the tripeptide sequence in the +3 position are changed to alanines, as recommended by the compilation of Gavel, Y., and von Heijne, G., Protein Engng. 5:433-442 (1990).
• Amino acid assignments of the Kabat consensus V K I/218/V H III SCA and A33/218 SCA are according to Kabat et al, Sequences of Proteins of Immunological Interest, pp. 108 & 331, 5th ed., U.S. Dept. Health and Human Services, Bethesda, MD (1991), where the assigned amino acid residue at a position is the most commonly occurring amino acid at that position.
• Amino acid assignments ofthe wild-type C6.5 variable domains are according to Schier, R., et al, J. Mol. Biol 255:28-43 (1996).
• the mutated SCAs are individually ligated into the Pichia transfer plasmid pHIL-Sl (Invitrogen Corp.) and transformed into Pichia pastoris. Detailed protocols for these procedures are presented in the Pichia Expression Kit Instruction Manual Cat. No. X1710-01 (1994) from Invitrogen Corporation.
• the SCA variants are placed behind a yeast signal sequence in these constructions and the integrated SCA in the yeast transformants are tested for secretion of the SCA protein or glycoprotein products. Evaluation of expression is done by Coomassie staining of SDS-PAGE gels. Further tests can be done to confirm expression of glycosylated SCAs as described in Example 1.
• the Pichia cells were harvested from a fermenter and centrifuged at 5000 rpm for 40 minutes. The clarified medium was collected and filtered through a 0.22 um filter. The sample was dialyzed against water with a membrane of molecular weight cut off of 3500 to a final conductivity of less than 1 mS. A cation exchange column (Poros-HS) was equilibrated with 15 mM Tris- Acetate at pH 6.15. The sample was adjusted to pH 6.2 and loaded onto the column.
• Poros-HS cation exchange column
• Glyco-CC49 was then eluted out with a salt concentration of 0.15 M NaCl in Tris- acetate buffer pH 7.4. It was then passed through a Poros-HQ column equilibrated with 0.15 M NaCl. Tris-acetate buffer pH 7.4. The flow through material was then processed on a size exclusion column (Pharmacia, Superdex- 75). The fractions corresponding to a molecular weight of 25-35 kDa were collected.
• PEGYLATION reaction is specific for the carbohydrate moiety and does not affect the single chain antigen binding molecule that contains no carbohydrate.
• the purified gCC49/3 (EN280) was concentrated to 2 mg/ml in 10 mM sodium acetate buffer pH 7. Just before the PEGYLATION reaction, the pH was adjusted to 5.5 by adding 1/10 volume of 1 M sodium acetate pH 5.5. Fresh sodium periodate prepared in acetate buffer pH 5.5 was then added to a final concentration of 10 mM. The protein was then oxidized for 1 hour in the dark at room temperature. At the end ofthe reaction, the sample was loaded onto a size exclusion column to remove unreacted sodium periodate. The protein was then concentrated to 2.5 mg/ml.
• PEG-hydrazide (5000 molecular weight) (Shearwater) made in the same buffer, at a molar excess of 140-fold over that of the protein, was added to the protein. The reaction was allowed to proceed at room temperature (25 °C) with shaking for 2.5 hours.
• the reaction product was fractionated on a size exclusion column.
• the purified products were than analyzed by SDS-PAGE ( Figure 13).
• SDS-PAGE analysis of glycosylated CC49/3 which either was un-modified or modified with PEG, shows that the PEG modified, glycosylated CC49/3 has a much higher molecular weight than the un-modified species. This indicates that glycosylated
• CC49/3 is also capable of being PEGylated.
• the percent retention in plasma was quantitated by ELISA methods.
• CC49/218 SCA was conjugated to SC-PEG of molecular mass 20,000 (the protocol is described in U.S. Patent 5,122,614, which disclosure is incorporated herein by reference).
• the average PEG:SCA molar ratio in the tested PEG-SCA conjugate was approximately 1 :1.
• the non-PEGylated CC49 SCA (Native-CC49), the biotinylated CC49 SCA (Bio-CC49), and the Triple-site Glycosylated CC49 SCA (Native GC; EN280) all have quite similar K d values of 3.6 nM, 6.2 nM, and 7.34 nM respectively.
• the PEGylated versions of the Triple-site Glyco-SCA showed reduced but substantial mucin-binding affinity.
• the P1B preparation with approximately 3 PEG polymers per SCA (EN280) has a K d of 48.37 nM.

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