# Patent

## Title
Methods for preparation of fucose-linked site specific conjugates of proteins with toxins, adjuvants, detection labels and pharmacokinetic half life extenders

## Abstract

The present invention relates to eukaryotic cells for producing molecules having an atypical fucose analog on their glycomoieties and/or amino acids. It also relates to methods for producing molecules having an atypical fucose analog on their glycomoieties and/or amino acids and to molecules obtainable by said methods. It further relates to methods for producing conjugates comprising molecules having an atypical fucose analog on their glycomoieties and/or amino acids and pharmaceutical active compounds and to conjugates obtainable by said methods. In addition, the present invention relates to specific conjugates.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is the U.S. National Stage entry of PCT/EP2012/060286, filed May 31, 2012, which claims priority to U.S. Provisional Application No. 61/491,456, filed May 31, 2011.


REFERENCE TO A SEQUENCE LISTING
This application includes a Sequence Listing named “95697-894485.txt” created on Jan. 29, 2014 and containing 27,000 bytes. The material contained in this text file is incorporated by reference in its entirety for all purposes.
The present invention relates to eukaryotic cells for producing molecules having an atypical fucose analogue on their glycomoieties and/or amino acids. It also relates to methods for producing molecules having an atypical fucose analogue on their glycomoieties and/or amino acids and to molecules obtainable by said methods. It further relates to methods for producing conjugates comprising molecules having an atypical fucose analogue on their glycomoieties and/or amino acids and pharmaceutical active compounds and to conjugates obtainable by said methods. In addition, the present invention relates to specific conjugates.
BACKGROUND OF THE INVENTION
Today, insertion of predetermined points of attachment for an active moiety plays a key role for efficient binding of biological products. Conjugation of proteins and functional compounds is typically accomplished through covalent attachment of the functional compound to side chains of amino acid residues. Classical bioconjugate technologies are known to work in a non-site-restricted fashion which makes it difficult to avoid undesirable couplings at critical amino acid residues and also poses a risk for lot consistency due to inherent heterogeneity of the outcome of the coupling reaction. Non-selective chemical coupling via hydroxyl-groups of protein-linked carbohydrate structures requires harsh reaction conditions and bears the risk of unwanted modification of amino acid side chains of the protein. Critical residues that may be affected by undesirable coupling or modification include amino acid side chains important for overall product thermal stability and aggregation propensity. In case of antibodies, unwanted conjugation to amino acid side chains within or in proximity to the complementarity determining regions (CDRs) may lead to reduced affinity and heterogeneous antigen-binding properties. Chemical coupling is typically accomplished via protein-linked functional groups such as primary amines, sulfhydryls, carbonyls, carbohydrates, carboxylic acids and hydroxyl groups. Reactive groups used for coupling via such functional groups include aryl azide, carbodiimide, carbonyl, diazirine, hydrazide, hydroxymethyl phosphine, imidoester, isocyanate, maleimide, N-hydroxy-succinimide ester (NHS-ester), pentafluorophenyl ester (PFP-ester), psoralen and pyridyl disulfide.
Conjugation can be easily directed at sulfhydryl groups. However, due to the reactivity of the thiol group, free thiols are rarely found in expressed proteins. Direct labeling of free thiol-groups thus relies mainly on the reduction of existing disulfide (S—S) bonds. Antibodies as one of the major groups of therapeutic proteins have been coupled to functional compounds via sulfhydryl groups in the past. Since reduction of the heavy to light chain disulfide bond occurs at approximately double the frequency of the heavy to heavy disulfide bonds, such partial reduction approaches bear the possible risk of protein fragmentation by light chain loss. (Sun, et al., Bioconjug Chem 16:1282-1290 (2005).) In particular, the thermal stability of the critical antibody CH2 domain may be negatively affected by reduction of the inter-sheet disulfide bond. Production of a homogenous product from such random-type sulfhydryl-coupling reaction is a rather complicated and inefficient process. Early preclinical versions of the cAC 10 antibody drug conjugate, a sulfhydryl-linked immunoconjugate involved linkage of eight cytotoxic drug molecules per antibody molecule (Doronina et al., Nat. Biotechnol. 21(7): 778-84 (2003)). The coupling-enabled cysteine residues were obtained by reduction of the four interchain disulfide bonds (Doronina et al., Nat. Biotechnol. 21(7): 778-84 (2003)). Incomplete reduction of disulfide bonds led to a heterogeneous mixture of incomplete conjugates with less than eight drug molecules loaded per antibody (Hamblett et. al. Effects of drug loading on the antitumor activity of a monoclonal antibody-drug conjugate. Clinical Cancer Research, 2004, 10(20):7063-70). Product homogeneity for the random sulfhydryl-coupled conjugate proofed difficult to achieve and overall yield was rather low (Hamblett et. al. 2004).
Coupling via amino-groups of lysine residues is also a common mode of producing bioconjugates of proteins and functional compounds. Most recently, a thiol-containing maytansinoid, DM1 (N-methyl-N-[3-mercapto-1-oxopropyl]-L-alanine ester of maytansinol), an analogue of the clinically-studied drug maytansine) was used to link maytansinoids to antibodies through disulfide bonds (Barginear and Budman, 2009) In the case of Trastuzumab-DM1, DM1 is linked to trastuzumab using the bifunctional reagent, SMCC(N-succinimidyl-4-maleimidomethyl-cyclohexanecarboxylate.) SMCC is first added to lysine residues on the protein to produce a linker modified antibody. Coupling of the succinimidyl-group of SMCC to lysine residues happens in a random fashion targeted at all surface exposed lysine residues of the antibody. The thiol group in DM1 is then reacted with the maleimide group of the linker to form the nonreducible thioether bond (Barginear and Budman, 2009). Maleimides react with sulfhydryls at pH 6.5-7.5 to form stable thioether bonds. At pH values>7.5, however, maleimides also react toward primary amines which can result in the production of undesired covalent protein oligomers. In addition, the random coupling of SMCC to the antibody results in a non-homogenous bioconjugate product. The C-terminal lysine of antibody heavy chains is prone to clipping during upstream cell culture production and thus further coupling heterogeneitiy may result from differentially clipped C-terminal lysine residues. Each Trastuzumab-DM1 antibody contains an average of 3.5 drug molecules (Smith S V. Technology evaluation, Hun90′-dml, immunogen. Curr Opin Mol Ther 2005; 7: 394-401.), reflecting the typical distribution from 0 to 8 drug molecules per antibody (Blattler W A, Chari R V J, Vite G D, Altmann K H, Eds. Anticancer Agents—Frontiers in Cancer Chemotherapy, American Chemical Society, Washington 2001; 317-38.). The stoichiometric molar ratio of antibody and functional compound is an important determinator of therapeutic activity and conjugate stability. Kulkarni et al. (Cancer Research 41:2700-2706 (1981)) found that the highest efficient antibody-to-toxin-ratio obtained for methotrexate was about ten methotrexate molecules per antibody, and that attempts to increase the drug-antibody molar ratio beyond this threshold decreased the yield of immunoconjugate and damaged antibody activity. Similar results have been reported by Kanellos et al. (JNC 75:319-329 (1985)).
The inherent inhomogeneity of random-coupled bioconjugate products poses a challenge for stability studies, lot consistency and in-process analytics. Production of a homogenous bioconjugate product from a random coupling reaction can only be accomplished with significant downstream effort associated with a dramatic loss of product yield. Thus, there is a need for antibodies having one or more predetermined sites for stoichiometric attachment of functional compounds.
Recently, such antibodies for predetermined, site-directed thiol-coupling were described by Seattle Genetics Inc. (United States Patent Application 2008/0305044). While this mode of coupling has all the benefits of a site-directed approach, the minor destruction of tertiary structure is likely to impact overall product thermal stability.
United States Patent Application 2010/0254943 AMINO ACID SUBSTITUTED MOLECULES and related applications belonging to the same patent family disclose a method for obtaining site specific conjugates of proteins by incorporating coupling enabled non-natural amino acids into the protein sequence and for utilizing such non-natural amino acid residues as an anchoring position for further chemical or biological modification. The amino acid position at which the non-natural amino acid is incorporated is specified by a codon that is typically used to specify a naturally occurring amino acid (such as a wobble codon, a bias codon, a sixth box codon, a 4 box codon, or any other sense codon that the host cell or in vitro translation system might be used to specify a non-natural amino acid incorporation site), or a codon which is typically a stop codon, such as amber, ochre, or opal, or a frameshift codon. In cases where in-frame stop codons are used for artificial incorporation of non-natural amino acids, the cells need to be knocked-out for the cognate release factor (or translation termination factor). Given the redundancy between the existing translation termination factors, cells will always produce both the correct full length protein containing the incorporated non-natural amino acids and also prematurely truncated versions of the target protein. This makes this type of production method for such coupling enabled proteins highly inefficient, particularly in eukaryotic expression systems where the release factor eRF1 functions as an omnipotent release factor and recognizes all three termination codons. While this method is suitable to produce proteins enabled for site directed and defined coupling, there is still a need to produce such defined coupling-enabled proteins at far higher process efficiency.
Glycan-Structures linked to naturally occupied N-glycosylation sites typically stabilize protein conformation. The size of the attached glycan apparently has only a very minor impact on protein thermal stability (Shental-Bechor and Levy, 2009) which makes naturally occurring N-Glycans an ideal linker for the conjugation of functional compounds—even if such compounds have a high molecular mass. In line with this, U.S. Pat. No. 7,138,371 and United States Patent Application 2010/0048456 disclose methods for conjugating polypeptides via the protein linked glycostructure to polyethylene glycol. Both of these documents as well as related applications and patents still did not solve the problem that leads to coupling heterogeneity.
Thus, there is still a need for homogenous and stable protein-pharmaceutically active compound-conjugates, wherein the pharmaceutically active compounds are coupled via an exactly defined moiety to the proteins. Particularly, site-directed coupling of pharmaceutically active compounds to proteins via a predetermined sugar attachment site is desirable. There is also still a need for cells for producing proteins which comprise such an exactly defined coupling moiety in high yields and which, thus, allow homogeneous and efficient coupling of pharmaceutically active compounds in a high degree, methods for producing such proteins using said cells, and methods for producing conjugates comprising such proteins and pharmaceutically active compounds.
The inventors of the present invention surprisingly found that homogenous, efficient, stable and site-directed coupling of pharmaceutically active compounds to molecules such as lipids or proteins can be achieved via an artificial core fucose analogue introduced into the glycostructure of said molecules. They also surprisingly found that homogenous, efficient, stable and site-directed coupling of pharmaceutically active compounds to proteins, e.g. glycoproteins, can be achieved via an artificial fucose molecule linked to a protein-O-fucusylation site incorporated in or attached to the amino acid sequence of said proteins. They particularly provide cells and methods which allow the production of said molecules, e.g. proteins or lipids, and conjugates between said molecules, e.g. proteins or lipids, and a pharmaceutically active compound in high yields. The produced conjugates are thermally stable and homogenous. The molecule can be a glycoengineered protein, a therapeutic protein, an antibody, a vaccine component, even a protein comprised in the envelope of an enveloped virus. The advantageous unifying concept is that the molecule, e.g. protein or lipid, is produced by a cell that is engineered for impaired innate fucosylation to its proteome so that exogenously added fucose is preferentially incorporated at a specific site, and that this exogenously added fucose is chemically activated so that further pharmaceutically active compounds can be selectively and covalently attached to said molecule. The added pharmaceutically active compound can be a compound that enhances or transforms the properties of the molecule, e.g. protein such as an anitbody or lipid, for example, it can increase cytotoxicity, increase biological half life, induce targeting of the molecule to specific tissues, protect against degradation or aggregation, induce or enhance innate or adaptive immunity, or increase or decrease infectivity of live viruses.
In one or more aspects, embodiments, preferred embodiments or more preferred embodiments of the present invention described below, the particular fucose analogue comprising molecules, e.g. proteins or lipids, or the particular fucose analogue-linked conjugates with site-specific attachment of a molecule, e.g. protein or lipid, and a pharmaceutically active compound (e.g. immunoconjugates) may have one or more of the following advantages:

    (I) A fucose analogue bound to the fucosylation site of the chitobiose core of proteins allows the coupling of a limited and defined number of pharmaceutically active compounds and, thus, enables the production of homogenously coupled conjugates. This positively influences product yield, lot consistency, therapeutic efficacy, and product comparability.
    (II) The fucose analogue has only a very minor impact on overall protein thermal stability. Thus, therapeutic efficacy by avoiding inactive compounds can be increased.
    (III) The artificial introduction of further defined N-glycosylation sites achieved due to the introduction of a single point mutation in the vicinity of a suitable asparagine residue, allows further site specific coupling of additional pharmaceutical compounds per protein molecule.
    (IV) To link the pharmaceutically active compound via a fucose analogue which is bound to the fucosylation site of the chitobiose core is advantageous as the distal part of a glycan is accessible to enzymatic degradation and hence coupling at those distal sites would result in instability of the conjugate. Chemical homogeneity and coupling stability of the conjugate is achieved by direct coupling of a pharmaceutically active compound to a fucose analogue monosaccharide bound at a defined position in the polypeptide chain (C glycan or O-glycan) or in the glycan structure. In case of an N-linked glycan, the core fucose, i.e. the particular fucose residue alpha-1,6-linked to the reducing end of the first N-acetylglucosamine residue of the chitobiose core of an N-glycan constitutes the shortest possible, defined and homogenous glyco-linker for such an N-linked-glycoconjugate.
    (V) The fucose analogue can be added to the culture medium. It is then taken up and further metabolized by conventional cells. However, the efficiency of the fucose de novo synthetic pathway starting from the abundant monosaccharide mannose (that itself is part of N glycans) provides 90% of the GDP fucose pool even in the presence of exogenous fucose and prevents efficient incorporation of fucose analogue into glycoproteins and inevitably results in a heterogeneous mixture of glycoproteins that are enabled for fucose-directed coupling to a low degree. Surprisingly, the inventors of the present invention found that cells with an interrupted biosynthesis pathway for fucose grown in a cell culture medium containing specific coupling-enabled fucose analogues efficiently incorporate the fucose analogue into glycoproteins produced in said cells. This results in a homogenous mixture of glycoproteins that are enabled for fucose-directed coupling to a high degree. In addition, the inventors found similar growth and performance parameters as the unmodified parental cell line grown in a medium not spiked with a coupling-enabled fucose analogue.
    (VI) Unlike other coupling technologies that rely on incorporation of coupling-enabled artificial amino acids or sugars into a produced protein, the technology described herein does not suffer from the associated process yield decline typically seen for such modified proteins. In particular, the inventors did not observe a block of core-fucosylation as it was described in previous patent applications concerning fucose alkyne or azido-fucose. In contrast thereto, the inventors observed an unexpected and efficient incorporation of azido-fucose.
    (VII) The covalent chemical bond between the protein bound fucose analogue and the conjugated pharmaceutically active compound is stable, not sensitive to mild reduction and therefore mitigates the risk of unwanted systemic release of the conjugated moiety.
    (VIII) Apart from antibody drug conjugates that kill target cells via the attached toxin cell mediated cytotoxicity, antibody dependent cellular cytotoxicity (ADCC) is the dominating mechanism of action of therapeutic antibodies, e.g. IgG1-type therapeutic antibodies. Such antibody molecules should either allow coupling of a toxin or be equipped for efficient ADCC. It is further desirable that a drug conjugated molecule is disabled for ADCC to avoid toxicity directed towards effector cells. It is, thus, desirable for toxin-linked conjugates to combine both action principles in a single drug in particular if an antibody coupling efficiency does not reach 100%. The present invention may provide a solution. Linking the drug via a fucose analogue will obliterate effector functions such as ADCC and uncoupled antibodies within an antibody composition produced in the cells disclosed herein will lack fucose and therefore provides enhanced ADCC.
    (IX) It is particularly advantageous if a fucose analogue which is directly linked to the polypeptide chain of a protein enables chemically homogenous coupling between said protein and a pharmaceutically active compound. This is achieved without modification of a protein that naturally contains a single or several protein-O-fucosylation sites. For proteins that do not contain protein-O-fucosylation sites or contain less sites than desired, the inventors of the present invention found the incorporation of an EGF-like repeat, representing such site, is very eligible.


SUMMARY OF THE INVENTION
In a first aspect, the present invention relates to a eukaryotic cell for producing a molecule comprising a fucose analogue, wherein

    (i) in said cell the GDP-L-fucose synthesis pathway originating from GDP-D-mannose is blocked, and
    (ii) said cell comprises a GDP-L-fucose analogue.


In a second aspect, the present invention relates to a method for producing a molecule which comprises a fucose analogue comprising the steps of:

    (i) providing a eukaryotic cell according to the first aspect, and
    (ii) isolating the molecule comprising a fucose analogue from the cell in i).


In a third aspect, the present invention relates to a molecule comprising a fucose analogue obtainable by the method of the second aspect.
In a fourth aspect, the present invention relates to a method for producing a conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound comprising the steps of:

    (i) carrying out the method of the second aspect, and
    (ii) covalently coupling a pharmaceutically active compound via the fucose analogue to the molecule comprising said fucose analogue.


In a fifth aspect, the present invention relates to a conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound obtainable by the method of the fourth aspect.
In a sixth aspect, the present invention relates to a conjugate which comprises a protein or polypeptide comprising one or more of the following structures:

—NG-cF*—Yo—C,

wherein each is attached to an N-glycosylation site comprised in said protein or polypeptide,

NG is an N-linked glycomoiety of said protein or polypeptide,

cF* is a core fucose analogue,

Y is a spacer unit, wherein o is an integer of 0 or 1, and

C is a pharmaceutically active compound.

In a seventh aspect, the present invention relates to a conjugate which comprises a protein or polypeptide comprising one or more EGF-like repeats comprising a serine and/or threonine residue to which the following structure:

—F*—Yp—C

is attached, wherein

F* is a fucose analogue moiety directly O-linked to said serine and/or threonine residue,

Y is a spacer unit, wherein p is an integer of 0 or 1, and

C is a pharmaceutically active compound.

This summary of the invention does not describe all features of the invention.
DETAILED DESCRIPTION OF THE INVENTION
Before the present invention is described in detail below, it is to be understood that this invention is not limited to the particular methodology, protocols and reagents described herein as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art.
Preferably, the terms used herein are defined as described in “A multilingual glossary of biotechnological terms: (IUPAC Recommendations)”, Leuenberger, H. G. W, Nagel, B. and Kölbl, H. eds. (1995), Helvetica Chimica Acta, CH-4010 Basel, Switzerland).
Several documents are cited throughout the text of this specification. Each of the documents cited herein (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, GenBank Accession Number sequence submissions etc.), whether supra or infra, is hereby incorporated by reference in its entirety. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
In the following, the elements of the present invention will be described. These elements are listed with specific embodiments, however, it should be understood that they may be combined in any manner and in any number to create additional embodiments. The variously described examples and preferred embodiments should not be construed to limit the present invention to only the explicitly described embodiments. This description should be understood to support and encompass embodiments which combine the explicitly described embodiments with any number of the disclosed and/or preferred elements. Furthermore, any permutations and combinations of all described elements in this application should be considered disclosed by the description of the present application unless the context indicates otherwise. The focus of the invention rests on a method for efficient production of site-specific fucose-linked glycoprotein conjugates. However, the particular features of the unique type of products attainable by this method are also of importance and specifically considered in example 1.
Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents, unless the content clearly dictates otherwise.
In the context of the present invention, the term “peptide” refers to a short polymer of amino acids linked by peptide bonds. It has the same peptide bonds as those in proteins, but is commonly shorter in length. The shortest peptide is a dipeptide, consisting of two amino acids joined by a single peptide bond. There can also be a tripeptide, tetrapeptide, pentapeptide, etc. A peptide is preferably one that is less than about 30 amino acids long and more preferably less than about 20 amino acids long.
The term “polypeptide”, as used herein, refers to a part of a protein which is composed of a single linear chain of amino acids bonded together by peptide bonds. Said chain of amino acids is preferably more than about 30 amino acids long or longer than 30 amino acids.
The term “protein”, as used herein, refers to a protein which comprises one or more polypeptides that resume a secondary and tertiary structure and additionally refers to a protein that is made up of several amino acid chains, i.e. several subunits, forming quaternary structures. The protein has sometimes non-peptide groups attached, which can be called prosthetic groups or cofactors.
The term “polypeptide fragment”, as used in the context of the present invention, refers to a polypeptide that has a deletion, e.g. an amino-terminal deletion, and/or a carboxy-terminal deletion, and/or an internally deletion compared to a full-length polypeptide.
In the context of the present invention, the term “fusion protein” refers to a protein comprising a polypeptide or polypeptide fragment coupled to heterologous amino acid sequences. Fusion proteins are useful because they can be constructed to contain two or more desired functional elements from two or more different proteins.
The terms “antibody”, “immunoglobulin”, “Ig” and “Ig molecule” are used interchangeably in the context of the present invention. The CH2 domain of each heavy chain contains a single site for N-linked glycosylation at an asparagine residue linking an N-glycan to the antibody molecule, usually at residue Asn-297 (Kabat et al., Sequence of proteins of immunological interest, Fifth Ed., U.S. Department of Health and Human Services, NIH Publication No. 91-3242). Included within the scope of the term are classes of Igs, namely, IgG, IgA, IgE, IgM, and IgD. Also included within the scope of the terms are the subtypes of IgGs, namely, IgG1, IgG2, IgG3 and IgG4. The terms are used in their broadest sense and include monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, single chain antibodies, and multispecific antibodies (e.g. bispecific antibodies).
The term “antibody fragment”, as used in the context of the present invention, refers to a fragment of an antibody that contains at least the portion of the CH2 domain of the heavy chain immunoglobulin constant region which comprises an N-linked glycosylation site of the CH2 domain. It may also be capable of specific binding to an antigen, i.e. chains of at least one VL and/or VH-chain or binding part thereof.
The terms “Fc domain” and “Fc region”, as used herein, refer to a C-terminal portion of an antibody heavy chain that interacts with cell surface receptors called Fc receptors and some proteins of the complement system. This property allows antibodies to activate the immune system.
In the context of the present invention, the term “glycoprotein” refers to proteins that contain oligosaccharide chains (glycans) covalently attached to their polypeptide side-chains. The carbohydrate is attached to the protein in a co-translational or posttranslational modification. This process is known as glycosylation such as N-glycosylation or O-glycosylation.
“N-glycosylation” means the addition of sugar chains which to the amide nitrogen on the side chain of asparagine. “O-glycosylation” means the addition of sugar chains on the hydroxyl oxygen on the side chain of hydroxylysine, hydroxyproline, serine, or threonine.
The term “glycolipid” as used in the context of the present invention refers to carbohydrate-attached lipids. They occur where a carbohydrate chain is associated with phospholipids on the exoplasmic surface of the cell membrane. The carbohydrates are found on the outer surface of all eukaryotic cell membranes. The carbohydrate structure of the glycolipid is controlled by the glycosyltransferases that add the lipids and glycosylhydrolases that modify the glycan after addition. Glycolipids also occur on the surface of enveloped viruses including those used as attenuated life vaccines.
The terms “glycan” or “glycomoiety” are used interchangeably in the context of the present invention to refer to a polysaccharide or oligosaccharide. The term “oligosaccharide” means a saccharide polymer containing a small number (typically three to ten) of component sugars, also known as simple sugars or monosaccharides. The term “polysaccharide” means a polymeric carbohydrate structure, formed of repeating units (either mono- or disaccharides, typically>10) joined together by glycosidic bonds. Glycans can be found attached to proteins as in glycoproteins or attached to lipids as in glycolipids. The terms encompass N-glycans, such as high mannose type N-glycans, complex type N-glycans or hybrid type N-glycans, O-glycans or
In the context of the present invention, the following monosaccharides are abbreviated as follows: Glucos=Glc, Galactose=Gal, Mannose=Man, Fucose=Fuc or F, N-acetylgalactosamine=GalNAc, or N-acetylglucosamine=GlcNAc, Fucose analogue=Fuc* or F*.
An “N-glycan” means an N-linked polysaccharide or oligosaccharide. An N-linked oligosaccharide is for example one that is or was attached by an N-acetylglucosamine residue linked to the amide nitrogen of an asparagine residue in a protein. The predominant sugars found on N-glycoproteins are glucose, galactose, mannose, fucose, N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc) and sialic acid (e.g., N-acetyl-neuraminic acid (NANA)). The processing of the sugar groups occurs co-translationally in the lumen of the ER and continues in the Golgi apparatus for N-linked glycoproteins. N-glycans have a common pentasaccharide core of Man3GlcNAc2 (“Man” refers to mannose; “Glc” refers to glucose; and “NAc” refers to N-acetyl; GlcNAc refers to N-acetylglucosamine). N-glycans differ with respect to the number of branches (antennae) comprising peripheral sugars (e.g., GlcNAc, galactose, fucose and sialic acid) that are added to the Man3GlcNAc2 core structure which is also referred to as the “trimannose core”, the “pentasaccharide core” or the “paucimannose core”. N-glycans are classified according to their branched constituents (e.g., high mannose, complex or hybrid).
A “high mannose type N-glycan” means an N-linked polysaccharide or oligosaccharide which has five mannose residues (Man5), or more mannose residues (e.g. Man6, Man7, or Man8).
A “complex type N-glycan” means a N-linked polysaccharide or oligosaccharide which typically has at least one GlcNAc attached to the 1,3 mannose arm and at least one GlcNAc attached to the 1,6 mannose arm of a “trimannose” core. Complex N-glycans may also have galactose (“Gal”) or N-acetylgalactosamine (“GalNAc”) residues that are optionally modified with sialic acid or derivatives (e.g., “NANA” or “NeuAc”, where “Neu” refers to neuraminic acid and “Ac” refers to acetyl). Complex N-glycans may also have intrachain substitutions comprising “bisecting” GlcNAc and core fucose (“Fuc”). Complex type N-glycans in the context of the present invention may contain zero (G0), one (G1), or two (G2) galactoses as well as one fucose attached to the first GlcNAc on the reducing end (denoted as G0F, G1F, G2F, respectively).
A “hybrid type N-glycan” means a N-linked polysaccharide or oligosaccharide which has at least one GlcNAc on the terminal of the 1,3 mannose arm of the trimannose core and zero or more mannoses on the 1,6 mannose arm of the trimannose core.
The abbreviations used in the context of the present invention to describe the glycostructures are defined as follows:

    core=Man3 GlcNAc2 
    G0=GlcNAc2 Man3 GlcNAc2 
    G0-GlcNAc=G0-structure missing one GlcNAc (i.e. GlcNAc Man3 GlcNAc2)
    G1=G0-structure containing one additional Galactose residue
    
        (i.e. Gal GlcNAc2 Man3 GlcNAc2)
    
    
    G2=G0-structure containing two additional Galactose residues (i.e. Gab GlcNAc2 Man3 GlcNAc2)
    G0F=G0-Structure containing an additional fucose-residue which is connected to the first GlcNAc-residue of the pentasaccharide core (i.e. GlcNAc2 Man3 GlcNAc2 Fuc)
    G0F-GlcNAc=G0-GlcNAc-structure containing an additional fucose-residue which is connected to the first GlcNAc-residue of the pentasaccharide core (i.e. GlcNAc Man3 GlcNAc2 Fuc)
    G1F=G1-structure containing an additional fucose-residue which is connected to the first GlcNAc-residue of the pentasaccharide core (i.e. Gal GlcNAc2 Man3 GlcNAc2 Fuc)
    G2F=G2-structure containing an additional fucose-residue which is connected to the first GlcNAc-residue of the pentasaccharide core (i.e. Gal2 GlcNAc2 Man3 GlcNAc2 Fuc)
    Man4=core-structure containing one additional Mannose residue
    
        (i.e. Man Man3 GlcNAc2)
    
    
    Man5=core-structure containing two additional Mannose residues
    
        (i.e. Manz Man3 GlcNAc2)
    
    
    Man6=core-structure containing three additional Mannose residues
    
        (i.e. Man3 Man3 GlcNAc2)
    
    
    Man7=core-structure containing four additional Mannose residues
    
        (i.e. Man4 Man3 GlcNAc2)
    
    
    Man8=(core-structure containing five additional Mannose residues
    
        (i.e. Man5 Man3 GlcNAc2).
    
    


To exemplarily describe glycostructures comprising a fucose analogue, the above mentioned F (fucose) can simply be replaced by F* (fucose analogue). For example, in case where an antibody with an N-glycan structure comprising a core Fucose analogue (cF*) is produced with the methods of the present invention.
An “O-glycan” means an O-linked polysaccharide or oligosaccharide. O-Linked glycans are usually attached to the peptide chain through serine or threonine residues. O-Linked glycosylation is a true post-translational event which occurs in the Golgi apparatus and which does not require a consensus sequence and no oligosaccharide precursor is required for protein transfer. The most common type of O-linked glycans contain an initial GalNAc residue (or Tn epitope), these are commonly referred to as mucin-type glycans. Other O-linked glycans include glucosamine, xylose, galactose, fucose, or mannose as the initial sugar bound to the Ser/Thr residues. O-Linked glycoproteins are usually large proteins (>200 kDa) that are commonly bianttennary with comparatively less branching than N-glycans.
Animal and human cells have fucosyltransferases that add a fucose residue to the GlcNAc residue at the reducing end of the N-glycans on a protein or to other nascent glycostructures on glycolipids. Fucosylation of protein- or lipid-bound glycomoieties requires a nucleotide sugar, GDP-L-fucose, as a donor and also the presence of particular fucosyl transferases, which transfer the fucosyl residue from the donor to the acceptor molecule (Becker and Lowe, 1999). In eukaryotic cells, e.g. vertebrate cells, GDP-L-fucose can be synthesized via two different pathways, either by the more prominent fucose de novo pathway or by the minor salvage pathway (Becker and Lowe, 1999). The salvage Pathway or “scavenger” pathway is a minor source of GDP-L-fucose (circa 10%) which can easily be blocked by omission of free fucose and fucosylated glycoproteins from the culture medium. The salvage pathway starts from extracellular fucose which can be transported into the cytosolic compartment via fucose-specific plasma membrane transporters. Alternatively, fucose cleaved from endocytosed glycoproteins can enter the cytosol. Cytosolic L-fucose is phosphorylated by fucokinase to fucose-1-phosphate and then converted by GDP-Fucose Pyrophosphorylase to GDP-L-fucose (FIG. 1, right hand panel). Cell culture experiments suggest that the salvage pathway makes a relatively minor contribution to the cytosolic GDP-L-fucose pools (Becker and Lowe, 1999).
The more prominent fucose de novo pathway starts from GDP-D-mannose and consists of a GDP-mannose dehydratase (GMD) and GDP-keto-deoxy-mannose-epimerase/GDP-keto-deoxy-galactose-reductase (GMER, also known as Fx in humans), both located in the cytoplasm, which in concert converts GDP-mannose to GDP-L-fucose (FIG. 1, left hand panel). Later, GDP-L-fucose is transported into the Golgi via a GDP-fucose transporter located in the membrane of the Golgi apparatus. Once GDP-L-fucose has entered the Golgi luminal compartment, fucosyltransferases can covalently link GDP-L-fucose to nascent glycomoieties within the Golgi. In particular, Fucosyltransferase (Fut8) transfers the fucose residue by means of an 1,6-linkage to the 6 position of the GlcNAc residue at the reducing end of the N-glycan.
As mentioned above, coupling of pharmaceutically active compounds to proteins, e.g. antibodies, in a stable, specific, homogenous and efficient manner is highly desirable in the medical field. Particularly, site-directed coupling of conjugates via predetermined attachment sites is desirable.
The inventors of the present invention surprisingly determined that homogenous, efficient, stable and site-directed coupling of pharmaceutically active compounds to molecules such as lipids or proteins (e.g. glycoproteins such as antibodies) can be achieved via an artificial core fucose analogue introduced into the glycostructure of said molecules. They also surprisingly found that homogenous, efficient, stable and site-directed coupling of pharmaceutically active compounds to proteins (e.g. glycoproteins such as antibodies) can be achieved via an artificial fucose analogue linked to a protein-O-fucosylation site incorporated in or attached to the amino acid sequence of said proteins. Moreover, said fucose analogues have the particular advantage that they allow, in contrast to natural fucose molecules, the specific coupling of pharmaceutically active compounds to molecules such as proteins or lipids, to which they are attached.
In addition, the inventors of the present invention surprisingly found that in a cell, wherein the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is blocked, molecules comprising a fucose analogue on its glycomoieties or amino acids instead of natural fucose can be produced in high yields. Reason for this is that any competitive incorporation of natural fucose is completely abolished in such a gycoengineered cell. The use of fucose-free medium and of a cell with obstructed fucose de-novo synthesis pathway leaves the fucose analogue as the exclusive substrate for fucosyltransferases present in such a cell. Moreover, since the natural GDP-fucose, the product of the fucose de novo synthesis pathway, is a competitive inhibitor of the salvage pathway fucose kinase, a block of the de novo synthesis additionally speeds up salvage pathway efficiency and, thus, the production of the metabolized GDP form of the fucose analogue which can be incorporated into molecules present in said cell, e.g. into nascent glycostructures of proteins. Accordingly, with a cell having an abolished fucose de novo synthesis pathway and comprising a fucose analogue, molecules such as proteins or lipids bearing a fucose analogue on its surface can be produced in a stoichiometrically efficient manner.
Thus, in a first aspect, the present invention provides a eukaryotic cell for producing a molecule comprising a fucose analogue, wherein

    (i) in said cell the GDP-L-fucose synthesis pathway originating from GDP-D-mannose is blocked, and
    (ii) said cell comprises a GDP-L-fucose analogue.


The term “a molecule which comprises a fucose analogue”, as used in the context of the present invention, refers to any compound which upon production in the eukaryotic cell of the present invention, preferably vertebrate cell, capable of adding a fucose analogue (instead of a natural fucose) to said compound, e.g. to its glycomoieties or amino acids, i.e. with an ability to add a fucose analogue (instead of a natural fucose) to said compound, e.g. to its glycomoieties or amino acids, comprises at least one fucose analogue, e.g. on its glycomoieties or amino acids. Such molecules comprise at least one or more sequence motifs recognized by a glycan transferring enzyme, e.g. comprising an Asp, Ser or Thr residue, preferably a tripeptide sequence Asn-X-Ser/Thr, wherein X is any amino acid except Pro. The glycan transferring enzyme comprised in the cell of the present invention is able to attach, if natural fucose is not available, also a fucose analogue to said molecules, e.g. to their glycomoieties or amino acids. In other words, a molecule which would naturally comprise a fucose molecule, e.g. on its glycomoieties or amino acids, after production in an unaltered cell, comprises upon production in the cell of the present invention a fucose analogue, e.g. on its glycomoieties or amino acids. A cell that produces molecules comprising amino acids or glycomoieties with natural fucose is, for example, a CHO, AGE1.HN, AGE1.CR, AGE1.CR.PIX, or AGE1.CS cell.
The skilled person can easily determine experimentally the presence of a fucose analogue and/or the amount of a fucose analogue on the glycomoieties of a particular molecule, e.g. an antibody molecule, by (i) cultivating cells of the present invention under conditions wherein the molecule of interest is produced, (ii) isolating said molecule from said cells and (iii) analysing the sugar chain structure of said molecule with respect to the fucose residues attached to its glycomoieties and determining the type of fucose residues and/or calculating the mean value of fucose residues present on the sugar chain structure of said molecule, and (iv) comparing the result with the result of the same molecule, e.g. an antibody molecule, produced in the same cells, wherein the molecule is produced with a fucose analogue-free pattern. Preferably, the cells used in the two experiments are identical but for the difference that one cell (the cell of the present invention) is cultured in the presence of a fucose analogue. Preferably both cells are cultivated under the identical culture conditions to exclude variations in fucosylation that may be due to differences in culture conditions. The same methodology can be used to determine experimentally the presence of a fucose analogue and/or the amount of a fucose analogue on the amino acid structure of a particular molecule, e.g. an antibody molecule.
The sugar chain structure in a molecule, e.g. antibody molecule, can simply be analyzed by the two dimensional sugar chain mapping method (Anal. Biochem., 171, 73 (1988), Biochemical Experimentation Methods 23—Methods for Studying Glycoprotein Sugar Chains (Japan Scientific Societies Press) edited by Reiko Takahashi (1989)). The structure deduced by the two dimensional sugar chain mapping method can be determined by carrying out mass spectrometry such as MALDI (Matrix Assisted Laser Desorption/Ionisation)-TOF-MS of each sugar chain.
The term that the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is “blocked”, as used herein, means that said pathway is blocked by at least 50%, preferably by at least 60% or 70%, more preferably by at least 80% or 90%, and most preferably by at least 95% or 100%, e.g. by at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%. The skilled person can easily determine experimentally the grade of de novo pathway blocking by determining the level of GDP-L-fucose produced in a cell wherein the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is blocked/interrupted and comparing it with the level of GDP-L-fucose produced in a cell wherein the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is not blocked/interrupted. In this context, for example, a reduction of the level of GDP-L-fucose by 50% compared to the level of GDP-L-fucose determined in a control cell means a blocking of the de novo pathway by 50% and a reduction of the level of GDP-L-fucose by 100% compared to the level of GDP-L-fucose determined in a control cell means a blocking of the de novo pathway by 100%. Preferably, the cells used in the two experiments are identical but for the difference that one cell (the cell of the present invention) comprises, for example, at least one enzyme which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate, wherein the enzyme does not catalyze the reaction which converts GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose in order to block the de novo pathway. Preferably both cells are cultivated under the identical culture conditions (e.g. culture medium or culturing time) to exclude variations in fucosylation that may be due to differences in culture conditions. It is particularly preferred that both cells are cultivated in the absence of an external fucose source to eliminate the influence of the salvage pathway on the amount of GDP-L-fucose produced in said cells. In addition, the skilled person knows how to determine the level of GDP-L-fucose to calculate the level/grade of blocking of the de novo pathway.
Blocking of the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) may be achieved in any way and at any step(s) (e.g. at one or more steps) in the de novo pathway provided that a reduced level of GDP-L-fucose (at least 50%), preferably no GDP-L-fucose, is produced from GDP-D-mannose in said cell (see above). This may be achieved due to (i) the mutation of enzyme(s) involved in said pathway so that their enzymatic activity is reduced or abolished, (ii) the knock-out or partial knock-out of gene(s) or promoter region(s) regulating said gene(s) so that no enzymatically active enzyme(s) involved in said pathway are produced or so that enzyme(s) with a reduced enzymatic activity involved in said pathway are produced, and/or (iii) the knock-down or partial knock-down of the mRNA(s) encoding said enzymes(s) with miRNA technology so that no so that no enzymatically active enzyme(s) involved in said pathway are produced or so that enzyme(s) with a reduced enzymatic activity involved in said pathway are produced (see FIG. 1, left hand panel). Said enzyme(s) could be, for example GDP-mannose dehydratase (GMD) and/or GDP-Fucose synthetase (GFS).
Fucosylation of molecules, e.g. proteins or lipids, comprising glycomoieties in eukaryotic cells (e.g. vertebrate cells) requires a nucleotide sugar, GDP-L-fucose, as a donor and also the presence of particular fucosyltransferases, which transfer the fucosyl residue from the donor to the acceptor molecule. As mentioned above, in eukaryotic cells (e.g. vertebrate cells) GDP-L-fucose can be synthesized via two different pathways, either by the more prominent fucose de novo pathway or by the minor salvage pathway.
In a preferred embodiment, the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is blocked, preferably to 80%, more preferably to 90% and most preferably to 95% or 100%, due to the presence of an enzyme (deflecting enzyme) in a eukaryotic cell (e.g. a vertebrate cell) which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate, but which does not catalyse the reaction which converts GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose. In this respect, it should be noted that the term “GDP-6-deoxy-D-lyxo-4-hexylose” is synonym with the term “GDP-4-keto-6-deoxy-D-mannose”. Both terms are used interchangeably herein.
Said enzyme present in the eukaryotic cell, e.g. vertebrate cell, can be any enzyme which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate under the proviso that said enzyme does not catalyze the reaction which converts GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose. Rather said enzyme converts GDP-6-deoxy-D-lyxo-4-hexylose into a product that can no longer be utilized for GDP-L-fucose synthesis in a eukaryotic cell, e.g. vertebrate cell. The enzyme which is preferably comprised in the eukaryotic cell, e.g. vertebrate cell, is an enzyme which is normally not present in said cell, i.e. a heterologous or artificial enzyme, e.g. an enzyme from an organism of another kingdom, such as from prokaryotes, preferably bacteria. Alternatively said enzyme can also be an enzyme which is normally present in a eukaryotic cell, e.g. vertebrate cell, but which does not covert the substrate GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose but rather into a different product, e.g. due to the presence of mutations.
The enzyme, which is preferably present in the eukaryotic cell, e.g. vertebrate cell, may be introduced into said cell, for example, via protein microinjection, protein electroporation or protein lipofection. It is also possible to introduce the nucleic acid sequence encoding the enzyme, preferably integrated in an expression vector, into the vertebrate cell, for example via DNA microinjection, DNA electroporation or DNA lipofection, which is subsequently transcribed and translated into the respective protein in the eukaryotic cell, e.g. vertebrate cell. The person skilled in the art is well informed about molecular biological techniques, such as microinjection, electroporation or lipofection, for introducing proteins or nucleic acid sequences encoding proteins into a eukaryotic cell, e.g. vertebrate cell, and knows how to perform these techniques.
It is preferred that two or more enzymes, i.e. 2, 3, 4, 5, 6 or 7, which use GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and which do not catalyze the conversion of GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose are present in a eukaryotic cell, e.g. vertebrate cell, to effectively block the fucose de novo pathway in said cell.
Preferably, the enzyme which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate is selected from the group consisting of GDP-6-deoxy-D-lyxo-4-hexylose reductase (synonym with GDP-4-keto-6-deoxy-D-mannose reductase, abbreviated RMD), GDP-perosamine synthetase (Per), GDP-6-deoxy-D-talose synthetase (GTS), GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), preferably GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) in combination with GDP-L-colitose synthase (ColC), and variants thereof, preferably the enzyme is from bacteria or derived from such a bacterial enzyme. More preferably, the enzyme which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate is a GDP-6-deoxy-D-lyxo-4-hexylose reductase (RMD), GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, and/or a GDP-perosamine synthetase (Per).
GDP-6-deoxy-D-lyxo-4-hexylose reductase (RMD) reduces the substrate GDP-6-deoxy-D-lyxo-4-hexylose to GDP-D-rhamnose. GDP-D-rhamnose is a nucleotide sugar donor for D-rhamnosylation in bacteria and does not occur in eukaryotes, e.g. vertebrates. Eukaryotic cells, e.g. vertebrate cells, also lack specific rhamnosyltransferases so that GDP-D-rhamnose can not be incorporated into nascent glycostructures of glycoproteins or glycolipids within eukaryotic cells, e.g. vertebrate cells.
The enzyme GDP-6-deoxy-D-talose synthetase (GTS) reduces the substrate GDP-6-deoxy-D-lyxo-4-hexylose to GDP-deoxy-D-talose. GDP-deoxy-D-talose is a nucleotide sugar donor for 6-deoxy-D-talosylation in bacteria and does not occur in eukaryotes, e.g. vertebrates. Eukaryotic cells, e.g. vertebrate cells, also lack specific deoxytalosyltransferases so that GDP-deoxy-D-talose can not be incorporated into nascent glycostructures within vertebrate cells.
Further, the enzyme GDP-perosamine synthetase (Per) reduces and transaminates the substrate GDP-6-deoxy-D-lyxo-4-hexylose to GDP-D-perosamine. GDP-D-perosamine is a nucleotide sugar donor for perosaminylation in bacteria, e.g. E. coli. GDP-D-perosamine is normally not present in eukaryotic cells, e.g. vertebrate cells. Eukaryotic cells, e.g. vertebrate cells also lack specific perosaminyltransferases so that GDP-D-perosamine can not be attached to nascent glycostructures within eukaryotic cells, e.g. vertebrate cells.
Therefore, the heterologous enzymes GTS and/or Per (i) deplete the substrate GDP-6-deoxy-D-lyxo-4-hexylose in the eukaryotic cell, e.g. vertebrate cell, and (ii) lead to the synthesis of artificial products (i.e. GDP-deoxy-D-talose in the case of GTS and GDP-D-perosamine in the case of Per) which can no longer be utilized for GDP-L-fucose synthesis.
Accordingly, a molecule which would usually comprise (natural) fucose on its glycomoieties and/or amino acids in a eukaryotic cell, wherein the de novo pathway is not blocked, and which is produced in the eukaryotic cell of the present invention, e.g. in a eukaryotic cell comprising GTS and/or Per and a fucose analogue, lacks (natural) fucose on its glycomoieties and/or amino acids, but comprises instead of (natural) fucose a fucose analogue on its glycomoieties and/or amino acids.
The enzyme GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) uses the substrate GDP-6-deoxy-D-lyxo-4-hexylose and converts it into GDP-4-keto-3,6-dideoxy-D-mannose. As the intermediate GDP-4-keto-3,6-dideoxy-D-mannose can be instable in eukaryotic cells, e.g. vertebrate cells, ColD is preferably used in combination with the enzyme GDP-L-colitose synthase (ColC). The enzyme ColC belongs to the class of GDP-4-dehydro-6-deoxy-D-mannose epimerases/reductases. The enzyme ColC further converts the intermediate GDP-4-keto-3,6-dideoxy-D-mannose into the stabile end-product GDP-L-colitose. Both products can not be incorporated into nascent glycostructures within eukaryotic cells, e.g. vertebrate cells, as said cells lack the respective glycosyltransferase to transfer GDP-4-keto-3,6-dideoxy-D-mannose and/or GDP-L-colitose to the glycomoieties of molecules present in said cells. Thus, it is preferred that ColD is present in the eukaryotic cell, e.g. vertebrate cell, in combination with ColC.
The enzyme GDP-Fucose synthetase (GFS) (also known as GDP-4-keto-6-deoxy-D-mannose epimerase/reductase, GMER) converts GDP-4-keto-6-deoxy-D-mannose into GDP-L-fucose in eukaryotic cells, e.g. vertebrate cells. The GFS reaction involves epimerizations at both C-3′′ and C-5′′ followed by an NADPH-dependent reduction of the carbonyl at C-4. An active site mutant, preferably GFS-Cys109Ser, is used in the present invention, which converts GDP-4-keto-6-deoxy-D-mannose into a product different from GDP-L-fucose, namely GDP-6-deoxy-D-altrose (see Lau S. T. B., Tanner, M. E. 2008. Mechanism and active site residues of GDP-Fucose Synthase, Journal of the American Chemical Society, Vol. 130, No. 51, pp. 17593-17602).
Preferably, two or more enzymes, i.e. 2, 3, 4, 5, 6, or 7, selected from the group consisting of GDP-6-deoxy-D-lyxo-4-hexylose reductase (RMD), GDP-perosamine synthetase (Per), GDP-6-deoxy-D-talose synthetase (GTS), GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), preferably GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) in combination with GDP-L-colitose synthase (ColC), and variants thereof are present in the eukaryotic cell, e.g. vertebrate cell.
A RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme variant which is preferred in the present invention differs from the RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme from which it is derived by up to 150 (i.e. up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, or 150) amino acid changes in the amino acid sequence (i.e. exchanges, insertions, deletions, N-terminal truncations and/or C-terminal truncations). The amino acid exchanges may be conservative or non-conservative. A RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme variant, which is preferred in the present invention can alternatively or additionally be characterised by a certain degree of sequence identity to the RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme from which it is derived. Thus, the RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme variants, which are preferred in the present invention have a sequence identity of at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to the respective reference RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme. Preferably, the sequence identity is over a continuous stretch of 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300 or more amino acids, preferably over the whole length of the respective reference RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme. It is particularly preferred that the sequence identity is at least 80% over the whole length, is at least 85% over the whole length, is at least 90% over the whole length, is at least 95% over the whole length, is at least 98% over the whole length, or is at least 99.5% over the whole length of the respective reference RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme. It is also particularly preferred that the sequence identity is at least 80% over at least 200 or 250 amino acids, is at least 85% over at least 200 or 250 amino acids, is at least 90% over at least 200 or 250 amino acids, is at least 95% over at least 200 or 250 amino acids, is at least 98% over at least 200 or 250 amino acids, or is at least 99.5% over at least 200 or 250 amino acids of the respective reference RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme.
A fragment (or deletion variant) of the RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme has preferably a deletion of up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, or 150 amino acids at its N-terminus and/or at its C-terminus and/or internally.
Additionally, a RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme having above indicated degree of relatedness to the reference enzyme is only regarded as a variant, if it exhibits the relevant biological activity to a degree of at least 30% of the activity of the respective reference enzyme. The relevant “biological activity” in the context of the present invention is the “enzyme activity”, i.e. the activity of the RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme variant to utilized the substrate GDP-6-deoxy-D-lyxo-4-hexylose and covert it into GDP-D-rhamnose, GDP-D-perosamine, GDP-deoxy-D-talose, GDP-6-deoxy-D-altrose, GDP-4-keto-3,6-dideoxy-D-mannose or GDP-L-colitose, respectively. The skilled person can readily assess whether a RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme variant has an enzyme activity of at least 30% of the enzyme activity of the respective reference RMD, Per, GTS, GFS-Cys109Ser, ColD, or ColC enzyme. Suitable assays, e.g. enzyme activity assays, for determining the “enzyme activity” enzyme variant compared to the enzyme activity of the respective reference enzyme are known to the person skilled in the art.
Preferably, the enzyme GDP-6-deoxy-D-lyxo-4-hexylose reductase (RMD) is from Pseudomonas aeruginosa (SEQ ID NO: 1). The enzyme GDP-6-deoxy-D-talose synthetase (GTS) is preferably from Actinobacillus actinomycetemcomitans (SEQ ID NO: 2). It is preferred that the enzyme GDP-perosamine synthetase (Per) is from Vibrio cholerae (SEQ ID NO: 3). Preferably, the GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) is from E. coli (SEQ ID NO: 4). The use of GDP-L-colitose synthase (ColC) from E. coli is also preferred (SEQ ID NO: 7). The wild-type GDP-Fucose synthetase (GFS) is from Cricetulus griseus (Chinese hamster) (SEQ ID NO: 5). The GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant from Cricetulus griseus (Chinese hamster) has the amino acid sequence of SEQ ID NO: 6.
As mentioned above, the invention encompasses variants of the enzymes using GDP-6-deoxy-D-lyxo-4-hexylose as a substrate. Thus, the present invention also covers variants of the above mentioned sequence identifier numbers, i.e. SEQ ID NO: 1 variants, SEQ ID NO: 2 variants, SEQ ID NO: 3 variants, SEQ ID NO: 4 variants, SEQ ID NO: 5 variants, SEQ ID NO: 6 variants, and SEQ ID NO: 7 variants. As to the structural and/or functional definition of said variants, it is referred to the aforementioned paragraphs.
The similarity of amino acid sequences, i.e. the percentage of sequence identity, can be determined via sequence alignments. Such alignments can be carried out with several art-known algorithms, preferably with the mathematical algorithm of Karlin and Altschul (Karlin & Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5877), with hmmalign (HMMER package, http//:hmmer.wustl.edu/) or with the CLUSTAL algorithm (Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic acids Res. 22, 4673-80) available e.g. on http://www.ebi.ac.uk/Tools/clustalw/ or on http://ebi.ac.uk/Tools/clustalw2/index.html or on http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pI?page=/NPSA/npsa_clustalw.html. Preferred parameters used are default parameters as they are set on http://www.ebi.ac.uk/Tools/clustalw/ or http://www.ebi.ac.uk/Tools/clustalw2/index.html. The grade of sequence identity (sequence matching) may be calculated using e.g. BLAST or BlastZ (or BlastX). A similar algorithm is incorporated into the BLASTP programs of Altschul et al. (1990) J. Mol. Biol. 215:403-410.
Preferably, the nucleic acid sequences of RMD, Per, GTS, ColD, ColC, or GFS-Cys109Ser are codon-optimized. The term “codon-optimized” as used in the context of the present invention means, for example, the removal of internal Tata boxes, chi sites, ribosome entry sites, RNA instability motifs, repeat sequences, intense RNA secondary structures and cryptic splice sites as well as the use of codons of higher utilization in eukaryotic (e.g. vertebrate) cells or of highly expressed genes in eukaryotic (e.g. vertebrate) cells.
The eukaryotic cell, e.g. vertebrate cell, further or alternatively to the enzyme comprises GDP-D-rhamnose, GDP-D-perosamine, GDP-deoxy-D-talose, GDP-6-deoxy-D-altrose, GDP-4-keto-3,6-dideoxy-D-mannose, and/or GDP-L-colitose to inhibit or prevent GDP-L-fucose synthesis as the inventors of the present invention have unexpectedly noticed that the supplementation, particularly the cytosolic supplementation, e.g. by intracytoplasmic injection, of the artificial sugars GDP-D-rhamnose, GDP-D-perosamine, GDP-deoxy-D-talose, GDP-6-deoxy-D-altrose, GDP-4-keto-3,6-dideoxy-D-mannose, and/or GDP-L-colitose positively contributes to the inhibition of fucose transfer in eukaryotic cells, e.g. vertebrate cells. The supplementation of the artificial sugar(s) GDP-6-deoxy-D-altrose, GDP-D-rhamnose, and/or GDP-D-perosamine is (are) particularly preferred.
It is preferred that the enzyme which uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and which does not catalyze the reaction which converts GDP-6-deoxy-D-lyxo-4-hexylose into GDP-L-fucose is expressed from a nucleic acid sequence transiently present or stably maintained in the vertebrate cell, e.g. episomally or chromosomally.
The nucleic acid sequence encoding the enzyme, preferably GDP-6-deoxy-D-lyxo-4-hexulose reductase (RMD), GDP-perosamine synthetase (Per), GDP-6-deoxy-D-talose synthetase (GTS), GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), or GDP-L-colitose synthase (ColC) is integrated in an expression vector, which is used to transform the cell.
Suitable expression vectors comprise plasmids, cosmids, bacterial artificial chromosomes (BAC) and viral vectors. Preferably, non-viral expression vectors are used.
The expression of the nucleic acid encoding the enzyme is controlled by expression control sequences. The term “expression control sequences” refers to nucleotide sequences which are affect the expression in eukaryotic cells (e.g. vertebrate cells) of coding sequences to which they are operably linked. Expression control sequences are sequences which control the transcription, e.g. promoters, TATA-box, enhancers; post-transcriptional events, e.g. polyadenylation; and translation of nucleic acid sequences. Preferably, the nucleic acid sequence encoding the above enzymes is under control of a constitutive promoter, preferably under control of a human translocation elongation factor 2 (EF2) promoter. Other constitutive promoters are well known in the art.
It is preferred that the nucleic acid sequence encoding the enzyme RMD, Per, GTS, GFS-Cys109Ser, ColD or ColC in the expression vector is operably inked to eukaryotic, e.g. vertebrate, specific expression control sequences, which allow the expression of the nucleic acid sequence encoding the enzyme RMD, Per, GTS, GFS-Cys109Ser, ColD or ColC in the eukaryotic cell, e.g. vertebrate cell. As a result, the enzyme(s) RMD, Per, GTS, GFS-Cys109Ser, and/or ColD, ColD preferably in combination with ColC, are expressed in the eukaryotic cell, e.g. vertebrate cell, of the present invention in yields optimal for the desired effect. Depending on the nature of the enzyme and the cell used for expression these yields may be high moderate or low. It is easy for those skilled in the art to choose appropriate eukaryotic, e.g. vertebrate specific expression control sequences, to achieve high, moderate or low level of expression.
As a result, a molecule which would usually comprise (natural) fucose on its glycomoieties and/or amino acids in a eukaryotic cell, wherein the de novo pathway is not blocked, and which is produced in the eukaryotic cell of the present invention, e.g. in a eukaryotic cell comprising GTS and/or Per and a fucose analogue, lacks (natural) fucose on its glycomoieties and/or amino acids, but comprises instead of (natural) fucose a fucose analogue on its glycomoieties and/or amino acids.
As mentioned above, the efficient production of molecules comprising a fucose analogue strongly benefits from a deficient fucose de novo synthesis pathway. The blocking of the de novo pathway avoids competitive incorporation of natural fucose and drastically increases incorporation efficiency for the fucose analogue. Other preferred embodiments to disrupt/block the de novo pathway are described below.
GDP-mannose dehydratase (GMD) is an enzyme which usually catalyzes the reaction which converts GDP-mannose into GDP-6-deoxy-D-lyxo-4-hexylose and GDP-Fucose synthetase (GFS) is an enzyme which usually uses GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and converts it into GDP-L-fucose (see FIG. 1, left hand panel). Thus, if no enzymatically active GMD and/or GFS is present in said cell, or if a GMD and/or GFS with a reduced enzymatic activity is present in said cell, the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is blocked.
Thus, alternatively or additionally, it is preferred that the eukaryotic cell of the present invention

    (i) does not comprise an enzymatically active GDP-mannose dehydratase (GMD) or comprises a GDP-mannose dehydratase (GMD) having a reduced enzymatic activity, and/or
    (ii) does not comprise an enzymatically active GDP-Fucose synthetase (GFS) or comprises a GDP-Fucose synthetase (GFS) having a reduced enzymatic activity. With the term “reduced enzymatic activity” of GMD or GFS, a reduction/lowering of the biological activity of GMD or GFS is meant, i.e. the activity of GMD to utilize the substrate GDP-mannose and to convert it into GDP-6-deoxy-D-lyxo-4-hexylose or the activity of GFS to utilized the substrate GDP-6-deoxy-D-lyxo-4-hexylose and to covert it into GDP-L-fucose. Preferably the biological activity of GMD or GFS is reduced by 50% or 60%, more preferably by at least 70% or 80%, and most preferably by at least 90%, 95% or 99%, e.g. at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%. Said enzyme activity reduction may be achieved due to the introduction of mutations such one or more, e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15, addition(s), deletion(s), insertion(s) and/or substitution(s) into the amino acid sequence. The skilled person can readily assess whether the enzyme activity of GMD or GFS (e.g. GMD or GFS mutants), is reduced compared to fully (100%) active GMDs or GFSs (e.g. non-mutated wild-type GMDs or GFSs). Suitable enzyme activity assays are known to the person skilled in the art. However, as mentioned above, the reduction of the enzyme activity of GMD and/or GFS has to be to such a degree/level that the GDP-L-fucose synthesis pathway originating form GDP-D-mannose (de novo pathway) is blocked by at least 50%, preferably by at least 60% or 70%, more preferably by at least 80% or 90%, and most preferably by at least 95% or 100% (see above).


As a result, a molecule which would usually comprise (natural) fucose on its glycomoieties and/or amino acids in a eukaryotic cell, wherein the de novo pathway is not blocked, and which is produced in the eukaryotic cell of the present invention, e.g. in a eukaryotic cell comprising GMD or GFS and a fucose analogue, lacks (natural) fucose on its glycomoieties and/or amino acids, but comprises instead of (natural) fucose a fucose analogue on its glycomoieties and/or amino acids.
In preferred embodiments, said cell does not comprise an enzymatically active GDP-mannose dehydratase (GMD) as

    (i) the GMD is mutated so that it is not able to catalyze the reaction which converts GDP-mannose into GDP-6-deoxy-D-lyxo-4-hexylose,
    (ii) the gene encoding GMD is partially or fully knocked-out so that no enzymatically active GMD is expressed which is able to catalyze the reaction which converts GDP-mannose into GDP-6-deoxy-D-lyxo-4-hexylose, or
    (iii) the promoter region regulating the expression of the GMD gene is partially or fully deleted so that no enzymatically active GMD is expressed which is able to catalyze the reaction which converts GDP-mannose into GDP-6-deoxy-D-lyxo-4-hexylose, and/or

said cell does not comprise an enzymatically active GDP-Fucose synthetase (GFS) as

    (i) the GFS is mutated so that it is not able to use GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and to convert it into GDP-L-fucose,
    (ii) the gene encoding GFS is partially or fully knocked-out so that no enzymatically active GFS is expressed which is able to use GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and to convert it into GDP-L-fucose, or
    (iii) the promoter region regulating the expression of the GFS gene is partially or fully deleted so that no enzymatically active GFS is expressed which is able to use GDP-6-deoxy-D-lyxo-4-hexylose as a substrate and to convert it into GDP-L-fucose.


It is also preferred to knock-down or to partially knock-down the enzymatic activity of GMD and/or GFS. The knock-down of the enzymatic activity of GMD and/or GFS may be achieved to the constitutive and stable expression of a specific siRNA or miRNA, e.g. episomally present in the cell, which blocks/inhibits the expression of GMD and/or GFS on the mRNA level.
The GMD and/or GFS mutants may be introduced into the eukaryotic cell of the present invention via protein microinjection, protein electroporation or protein lipofection. It is also possible to introduce the nucleic acid sequence encoding the GMD mutant and/or the nucleic acid sequence encoding the GFS mutant, preferably integrated in an expression vector, into the eukaryotic cell of the present invention via DNA microinjection, DNA electroporation, or DNA lipofection. In preferred embodiments, the GMD mutant and/or GFS mutant is expressed from a nucleic acid sequence transiently present or stable present in the eukaryotic cell of the present invention.
It is further preferred that the fucose salvage pathway is additionally blocked in the eukaryotic cell. Therefore, it is preferred to use growth media free of fucose and of fucosylated glycoproteins, when culturing the eukaryotic cells, e.g. vertebrate cells, of the present invention.
The growth medium or culture medium is instead spiked with a fucose analogue which is taken up by the eukaryotic cell, e.g. vertebrate cell, of the present invention (e.g. by active transport or passive diffusion), which is tolerated and metabolized by the eukaryotic cell, e.g. vertebrate cell, of the present invention via the salvage pathway, and which stable enough to be linked, instead of natural fucose, to the glycomoieties and/or amino acids in upstream cell culturing processes.
It is preferred that the eukaryotic cell, e.g. vertebrate cell, of the present invention further comprises at least one (acceptor) molecule which is/is capable of being a substrate for a fucosyltransferase (e.g. protein or lipid).
The term “(acceptor) molecule being/capable of being a substrate for a fucosyltransferase”, as used in the context of the present invention, refers to any compound of interest, e.g. a protein, polypeptide, peptide, lipid, lipid fragment, or fusion protein, comprising glycomoieties and/or amino acids to which at least one fucose residue is attached, if produced in a cell having an unaltered fucosylation activity. Such a compound is a suitable substrate for a fucosyltransferase. A preferred (acceptor) molecule is accordingly a glycoprotein, glycopolypeptide, glycopeptide, glycolipid, glycolipid fragment, or glycosylated fusion protein. The term “(acceptor) molecule capable of being a substrate for a fucosyltransferase”, as used in the context of the present invention, also refers to any compound of interest, e.g. a protein, polypeptide, peptide, lipid, lipid fragment, or fusion protein, so long as it is a prospective glycosylated compound, e.g. glycoprotein, glycopolypeptide, glycopeptide, glycolipid, glycolipid fragment, or glycosylated fusion protein to which at least one fucose residue can be attached, if produced in a cell having an unaltered fucosylation activity. Preferably the protein is not of prokaryotic origin. It is particularly preferred that the protein is a mammalian protein or derived therefrom.
The presence of a molecule capable of being a substrate for a fucosyltransferase in the eukaryotic cell, e.g. vertebrate cell, of the present invention, i.e. in a cell in which the de novo pathway is blocked and in which the salvage pathway is preferably additionally inhibited due to culturing in fucose deficient medium but which comprises a fucose analogue, leads to the production of a molecule which does not comprise (natural) fucose on its glycomoieties and/or amino acids but which comprises a fucose analogue on its glycomoieties and/or amino acids.
Thus, said molecule (e.g. protein or lipid) may be a molecule which (i) naturally comprises (natural) fucose on its glycomoieties and/or (ii) comprises a protein-O-fucosyltransferase recognition site in its structure (e.g. amino acid sequence).
Said protein-O-fucosyltransferase recognition site may be a naturally occurring recognition site such as a recognition site naturally present in the molecule structure (e.g. amino acid sequence), or may be a non-naturally occurring (artificial) recognition site such as a recognition site additionally introduced into the molecule structure (e.g. amino acid sequence) of said molecule (e.g. protein or lipid).
Preferably, said molecule (e.g. protein) comprises (e.g. naturally and/or artificially) one or more EGF-like repeats, e.g. 1, 2, 3, 4, 5, 6, 7, or 8, preferably 1 or 2, comprising a serine and/or threonine residue which is (are) recognized by a protein-O-fucosyltransferase, preferably by POFUT1. Said enzyme may add fucose sugars in O-linkage to serine or threonine residues between the second and third conserved cysteines in said EGF-like repeats. The protein is an inverting glycosyltransferase, which means that the enzyme uses GDP-L-fucose as a donor substrate and transfers the fucose in O-linkage to the protein producing fucose-α-O-serine/threonine. In the eukaryotic cell of the present invention, i.e. in a cell in which the de novo pathway is blocked and in which the salvage pathway is preferably additionally inhibited due to culturing in fucose deficient medium but which comprises a fucose analogue, said enzyme, i.e. the protein-O-fucosyltransferase, preferably POFUT1, attaches (preferentially or exclusively) a fucose analogue instead of (natural) fucose to its recognition sites.
More preferably, said EGF-like repeat is an EGF-like repeat with an amino acid sequence according to SEQ ID NO: 10 or a variant thereof which is at least 80% or 85%, more preferably 90% or 95%, most preferably 98% or 99%, e.g. 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 95, 96, 97, 98, or 99%, identical to said amino acid sequence. In preferred embodiments, the sequence identity is over a continuous stretch of at least 10, 12, 15, 17, 20, 22 or more amino acids, preferably over the whole length of the respective reference polypeptide (SEQ ID NO: 10). In particularly preferred embodiments, the sequence identity is at least 95% over the whole length, is at least 96% over the whole length, is at least 97% over the whole length, is at least 98% over the whole length, or is at least 99% over the whole length of the respective reference polypeptide (SEQ ID NO: 10). It is further particularly preferred that the above-mentioned variant is a functionally active variant. This means that the variations, e.g. in form of one or more, e.g. 1, 2, 3, 4, or 5, amino acid substitution(s), addition(s), insertion(s), and/or deletion(s), lie outside of the amino acid position(s) described above allowing the recognition of the protein-O-fucosylation site and/or the attachment of a fucose analogue to said site by a protein-O-fucosyltransferase. The person skilled in the art is aware of techniques how to assess whether a fucose analogue can still be attached to the EGF-like repeat variant comprised in the above mentioned molecules. One suitable technique is, for example, MALDI-TOF/TOF.
Most preferably, said EGF-like repeat (e.g. SEQ ID NO: 10 or a variant thereof) is attached to/comprised at the C-terminus and/or N-terminus of the molecule, e.g. protein.
It is, additionally or alternatively, further preferred that said molecule (e.g. protein) comprises (e.g. naturally and/or artificially) one or more thrombospondin repeats comprising a serine and/or threonine residue which is (are) recognized by a protein-O-fucosyltransferase, preferably by POFUT2. Said enzyme may add fucose sugars in 0 linkage to serine or threonine residues in Thrombospondin repeats. The protein is an inverting glycosyltransferase, which means that the enzyme uses GDP-L-fucose as a donor substrate and transfers the fucose in O linkage to the protein producing fucose-α-O-serine/threonine. In the eukaryotic cell of the present invention, i.e. in a cell in which the de novo pathway is blocked and in which the salvage pathway is preferably additionally inhibited due to culturing in fucose deficient medium but which comprises a fucose analogue, said enzyme, i.e. the protein-O-fucosyltransferase, preferably POFUT2, attaches (preferentially or exclusively) a fucose analogue instead of (natural) fucose to its recognition sites.
The term “a molecule which naturally comprises fucose on its glycomoieties”, as used in the context of the present invention, refers to any compound which upon production in a eukaryotic cell, e.g. vertebrate cell, capable of adding fucose to glycomoieties, i.e. with an unaltered ability to add fucose to glycomoieties, comprises glycomoieties comprising at least one fucose residue. Such molecules comprise at least one or more sequence motifs recognized by a glycan transferring enzyme, e.g. comprising an Asp, Ser or Thr residue, preferably a tripeptide sequence Asn-X-Ser/Thr, wherein X is any amino acid except Pro. Preferred examples of cells (e.g. eukaryotic cells such as vertebrate cells) that produce molecules comprising glycomoieties with fucose are CHO, AGE1.HN, AGE1.CR, AGE1.CR.PIX, or AGE1.CS. Preferably such compounds are proteins fusion proteins or lipids. Preferably the proteins are of eukaryotic, preferably vertebrate most preferably of mammalian origin or derived therefrom. In the eukaryotic cell of the present invention, i.e. in a cell in which the de novo pathway is blocked and in which the salvage pathway is preferably additionally inhibited due to culturing in fucose deficient medium but which comprises a fucose analogue, said molecule comprises (preferentially or exclusively) a fucose analogue instead of (natural) fucose on its glycomoieties.
The molecule capable of being a substrate for a fucosyltransferase may also be a viral component. Said viral component can be any glycosylated entity such as that contained in an enveloped live virus, whether attenuated or wild type, an inactivated or split dead enveloped virus, an isolated or purified viral glycoprotein or a viral glycolipid, or a glycoprotein that is encoded and produced by a viral expression vector with which a producer cell is infected. To obtain a virus that has incorporated the fucose analogue on its viral components, the cell according to the present invention has to be used, i.e. a cell engineered for block in de novo synthesis of fucose and preferably also for abolished alpha-1,3-fucosyltransferase activity.
It is preferred that the molecule capable of being a substrate for a fucosyltransferase is a protein or polypeptide, preferably an endogenous or exogenous protein or polypeptide. The term “exogenous protein or polypeptide” means any protein or polypeptide that is either coming from the outside of the respective cell or that is expressed inside the cell from a nucleic acid introduced into the respective cell. The term “endogenous protein or polypeptide” refers to any protein that is encoded by the genome of the cell. Preferably, the protein or polypeptide of interest, namely the prospective glycoprotein or glycopolypeptide, is recombinantly expressed in the eukaryotic cell. It is preferred that said protein or polypeptide is expressed from a nucleic acid sequence transiently present or stably maintained in the eukaryotic cell. Suitable expression vectors and expression control sequences have been described above with respect to the enzyme. These can equally be used in the context of the expression of the nucleic acid encoding the protein of interest.
Thus, in a preferred embodiment of the present invention, the eukaryotic cell, e.g. vertebrate cell, comprises

    (i) at least one polynucleotide comprising a nucleic acid sequence encoding the enzyme GDP-6-deoxy-D-lyxo-4-hexylose reductase (RMD), GDP-perosamine synthetase (Per), GDP-6-deoxy-D-talose synthetase (GTS), GDP-Fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), or GDP-L-colitose synthase (ColC), operably linked to specific expression control sequences, which allow the expression of the nucleic acid sequence encoding the respective enzyme, and
    (ii) at least one polynucleotide comprising a nucleic acid sequence encoding the protein of interest, namely the prospective glycoprotein, e.g. an antibody, such as IgG1, operably linked to specific expression control sequences, which lead to expression of the nucleic acid sequence encoding the protein of interest, e.g. an antibody, such as IgG1, in said cell.


As a result, (i) the enzyme(s) RMD, Per, GTS, GFS-Cys109Ser, and/or ColD, ColD preferably in combination with ColC, and (ii) the protein(s) of interest, namely the prospective glycoprotein(s), e.g. an antibody, such as IgG1, are expressed in the eukaryotic cell, e.g. vertebrate cell, of the present invention.
The polynucleotides mentioned above may be introduced via transfection, electroporation or lipofection into the cell. The transfection, electroporation or lipofection may be performed according to standard procedures known to the person skilled in the art. Following the introduction of foreign nucleic acids, transfected, electroporated or lipofected cells may be selected by applying selective pressure by adding, for example, antibiotics, e.g. G418, puromycin, neomycin or geneticin, to the culture medium. Suitable selection systems are well known in the art.
Preferably, the protein or polypeptide is an antigen binding protein or polypeptide, preferably an antibody, more preferably an IgG1 antibody, an antibody fragment, more preferably an antibody fragment comprising the Fc region of an antibody, an antibody fusion protein, more preferably an antibody fusion protein comprising the Fc region of an antibody, a virus protein, virus protein fragment, or an antigen. Another preferred protein is an enzyme, a cytokine, a lymphokine, an agonist, an antagonist, or a hormone.
Specific examples of desired proteins or polypeptides include, but are not limited to, insulin, insulin-like growth factor, hGH, tPA, cytokines, such as interleukines (IL), e.g. IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, interferon (IFN) alpha, IFN beta, IFN gamma, IFN omega or IFN tau, tumor necrosisfactor (TNF), such as TNF alpha and TNF beta, TNF gamma, TRAIL, G-CSF, GM-CSF, M-CSF, MCP-I and VEGF. Also included is the production of erythropoietin or any other hormone growth factor. Preferably, the afore-mentioned molecules have a therapeutic and/or diagnostic use.
The antibody may be a monoclonal antibody (including a full length antibody) or a polyclonal antibody. Preferably, the antibody or antibody fragment is selected from the group consisting of IgG (e.g. IgG1, IgG2, IgG3 and IgG4), IgA, IgE, IgM, and IgD, single chain antibodies, single domain antibodies, multispecific antibodies (e.g. bispecific antibodies), scFv, dsFv, scFab, a maxibody, nanobody, transbody, diabody, adnectin, evibody, DARpin, affibody, ankyrin, iMab, camelid-antibody, glycosylated single-domain antigen-binding fragments derived from a Camelid heavy chain-only antibody, an engineered lipocalin-type protein such as an anticalin, an affilin, or a Kunitz-domain, and knottin, followed by at least one, preferably two constant domains (Fc) of an immunoglobulin, preferably of human origin.
Preferably, the antibody or antibody fragment is

    (i) a naturally occurring antibody or antibody fragment,
    (ii) a non-naturally occurring antibody or antibody fragment, preferably an antibody mutant or antibody fragment mutant.


Said antibody mutant or antibody fragment mutant may also be designated as modified antibody or modified antibody fragment. Said naturally occurring antibody or naturally occurring antibody fragment may also be designated as non-modified antibody or non-modified antibody fragment.
In preferred embodiments, the (naturally occurring or modified) antibody comprises two heavy chains or the (naturally occurring or modified) antibody fragment comprises a heavy chain, more preferably the constant domain of a heavy chain (CH domain).
It is particularly preferred that the naturally occurring antibody comprises two heavy chains wherein each heavy chain has a naturally N-glycosylation site at asparagine N297 (numbered according to the Kabat numbering system), or that the naturally occurring antibody fragment comprises a heavy chain, more preferably the constant domain of a heavy chain (CH domain), having a naturally N-glycosylation site at asparagine N297 (numbered according to the Kabat numbering system).
It is further particularly preferred that the modified antibody comprises two heavy chains wherein each heavy chain has an artificial N-glycosylation site at asparagine N159, particularly generated due to the replacement of G161 by S161, and/or an artificial N-glycosylation site at asparagine N276, particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system), or that the modified antibody fragment comprises a heavy chain, more preferably the constant domain of a heavy chain (CH domain), having an artificial N-glycosylation site at asparagine N159, particularly generated due to the replacement of G161 by S161, and/or an artificial N-glycosylation site at asparagine N276, particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system).
Preferably, the above mentioned modified antibodies or modified antibody fragments differ from their respective wild-type/unmodified antibodies or antibody fragments in that they comprise, per heavy chain, more preferably per constant domain of a heavy chain (CH domain), one or more, e.g. 1, 2, 3, 4, 5, 6, 7, or 8, preferably 1, 2, 3, or 4, additional functional N-glycosylation sequons. This is particularly useful for the attachment of additional artificial N-glycans. Thus, said modified antibodies or modified antibody fragments can provide more than the two N-glycosylation sequons which may normally be present per antibody molecule (one per heavy chain or CH domain). This in turn allows the coupling of more than two fucose analogues per antibody molecule (one per heavy chain or CH domain) which can be attached to the additional artificial N-glycans.
The term “sequon”, as used herein, refers to a sequence of three consecutive amino acids in a protein or polypeptide that can serve as the attachment site to a polysaccharide (sugar) called an N-linked-glycan. This is a polysaccharide linked to the protein or polypeptide via the nitrogen atom in the side chain of asparagine (Asn). A sequon is either Asn-X-Ser or Asn-X-Thr, where X is any amino acid except proline.
Thus, it is also particularly preferred that the modified antibody comprises two heavy chains wherein each heavy chain has a naturally N-glycosylation site at asparagine N297 and further an artificial N-glycosylation site at asparagine N159, particularly generated due to the replacement of G161 by S161, and/or an artificial N-glycosylation site at asparagine N276, particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system), or that the modified antibody fragment comprises a heavy chain, more preferably the constant domain of a heavy chain (CH domain), having a naturally N-glycosylation site at asparagine N297 and further an artificial N-glycosylation site at asparagine N159, particularly generated due to the replacement of G161 by S161, and/or an artificial N-glycosylation site at asparagine N276, particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system).
Accordingly, in a preferred embodiment, an antibody comprising two heavy chains or an antibody fragment comprising a heavy chain (H), preferably the constant domain of a heavy chain (CH domain), comprises one or more N-glycosylation sites selected from the group consisting of asparagine N297, asparagine N159 and asparagine N276 (all numbered according to the Kabat numbering system). In a particularly preferred embodiment, an antibody comprising two heavy chains comprises 1, 2, or 3 N-glycosylation sites selected from the group consisting of asparagine N297, asparagine N159 and asparagine N276 (all numbered according to the Kabat numbering system) per heavy chain, or an antibody fragment comprising a heavy chain (H), preferably the constant domain of a heavy chain (CH domain), comprises 1, 2, or 3 N-glycosylation sites selected from the group consisting of asparagine N297, asparagine N159 and asparagine N276 (all numbered according to the Kabat numbering system). As mentioned above, the N-glycosylation site at asparagine N159 is particularly generated due to the replacement of G161 by S161 and the N-glycosylation site at asparagine N276 is particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system).
More preferably, the antibody or antibody fragment comprises an antibody heavy chain constant domain having an amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein the amino acids G161 (CH) and/or Y278 (CH) (numbered according to the Kabat numbering system) are substituted with serine. These substitutions allow the N-glycosylation at asparagine N159 and/or N276 (see above). Said antibody or antibody fragment may also comprise a functional naturally occurring N-glycosylation site at asparagine N297 (CH) (numbered according to the Kabat numbering system). Thus, such modified antibody may enable the defined attachment of between two to six fucose analogues, or such modified antibody fragment may enable the defined attachment of between one to three fucose analogues.
Also preferred are variants of the amino acid sequence according to SEQ ID NO: 8 (IgG1 CH Allele 01, human), wherein the amino acids G161 (CH) and/or Y278 (CH) (numbered according to the Kabat numbering system) are substituted with serine, which are at least 90%, more preferably at least 95%, most preferably at least 99%, e.g. 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%, identical to said amino acid sequence, or variants of the amino acid sequence according to SEQ ID NO: 9 (IgG1 CH Allele O2, human), wherein the amino acids G161 (CH) and/or Y278 (CH) (numbered according to the Kabat numbering system) are substituted with serine, which are at least 90%, more preferably at least 95%, most preferably at least 99%, e.g. 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%, identical to said amino acid sequence. In preferred embodiments, the sequence identity is over a continuous stretch of at least 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 120, or more amino acids, preferably over the whole length of the respective reference polypeptide. In particularly preferred embodiments, the sequence identity is at least 95% over the whole length, is at least 96% over the whole length, is at least 97% over the whole length, is at least 98% over the whole length, or is at least 99% over the whole length of the respective reference polypeptide.
It is further particularly preferred that the afore-mentioned variants are functionally active variants. This means that the variations, e.g. in form of one or more, e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15, amino acid substitution(s), addition(s), insertion(s), and/or deletion(s) in the above indicated ranges, lie outside of the amino acid position(s) or differ from the amino acid position(s) described above allowing the recognition of a N-glycosylation site and the attachment of additional artificial N-glycans and/or naturally occurring N-glycans to said site. This means that (i) a functionally active variant of the amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein G161 is replaced by S161 generating an N-glycosylation site at asparagine N159, has no amino acid variations at these positions by may vary in other amino acid positions within the above indicated ranges, (ii) a functionally active variant of the amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein Y278 is replaced by S278 generating an N-glycosylation site at asparagine N276 has no amino acid variations at these positions by may vary in other amino acid positions within the above indicated ranges, (iii) a functionally active variant of the amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein G161 is replaced by S161 generating an N-glycosylation site at asparagine N159 and Y278 is replaced by S278 generating an N-glycosylation site at asparagine N276 has no amino acid variations at these positions by may vary in other amino acid positions within the above indicated ranges. Said functional variants may further comprise an N-glycosylation site at asparagine N297 which is not mutated (all numbered according to the Kabat numbering system).
In other words, in the above-mentioned functionally active variants, the sequence motif(s) recognized by a glycan transferring enzyme, e.g. comprising an Asp, Ser or Thr residue, preferably a tripeptide sequence Asn-X-Ser/Thr, wherein X is any amino acid except Pro, is still present and not mutated.
The person skilled in the art is aware of techniques how to assess whether N-glycans can still be attached to the additional artificial N-glycans and/or naturally occurring N-glycans comprised in the above mentioned antibody or antibody fragment variants and, thus, whether a fucose analogue can still be coupled. One suitable technique is, for example, MALDI-TOF/TOF.
With respect to the Kabat numbering scheme it is referred to Kabat et al., 1983 E. A. Kabat, T. T. Wu, H. Bilofsky, M. Reid-Miller and H. Perry, Sequence of Proteins of Immunological Interest, National Institutes of Health, Bethesda (1983)). Although the boundaries of the Fc region may vary, the human IgG heavy chain Fc region is usually defined to comprise residues C226 or P230 to its carboxyl-terminus, wherein the numbering is according to the EU index as in Kabat et al. (1991, NIH Publication 91-3242, National Technical Information Service, Springfield, Va.). The “EU index as set forth in Kabat” refers to the residue numbering of the human IgG1 EU antibody as described in Kabat et al.
Preferably, the virus protein or virus protein fragment is comprised in the envelope membrane of an enveloped virus. It is particularly preferred that the virus protein is G or F protein from Respiratory Syncytial Virus and that the virus protein fragment is the extracellular fragment of said protein. A further aspect of the invention is a virus comprising said virus protein or virus protein fragment.
It is also preferred that the molecule capable of being a substrate for a fucosyltransferase is a lipid. Preferably, the lipid is a glyceroglycolipid, most preferably a galactolipid, a sulfolipid (SQDG), or a glycosphingolipids, most preferably a cerebroside (e.g. a galactocerebroside or a glucocerebroside), a ganglioside, a globoside, a sulfatide or a glycophosphosphingolipid.
The glycosphingolipid (GSL) is particularly preferred. Glycosphingolipids contain a hydrophobic ceramide anchor N-acylsphingosine and a hydrophilic head-group composed of saccharides. They are normally found at the outer surface of cell membranes. The composition of the saccharide-moiety is cell type specific and depends on the developmental stage of the organism or can change with the oncogenic state of a cell.
It is particularly preferred that the lipid is comprised in the envelope membrane of an enveloped virus.
A further aspect of the invention is a virus comprising said lipid. Another further aspect of the invention is a virus comprising said lipid and said protein. Most preferably, the virus protein and/or lipid are comprised in the envelope of an enveloped virus. As already mentioned above, the protein or lipid can be a virus protein or lipid which is comprised in the envelope membrane of an enveloped virus. Preferably, the enveloped virus is used entirely or in part as an active component of a viral vaccine. The term “viral vaccine” means a preparation of a weakened or killed virus that upon administration stimulates antibody production or cellular immunity against the virus but is incapable of causing severe infections.
The above mentioned virus can be introduced into the eukaryotic cell, e.g. vertebrate cell, via virus infection. The virus can also be introduced into the eukaryotic cell, e.g. vertebrate cell, by introducing nucleic acids encoding all or part of the virus to be produced. In the case it will be necessary to provide proteins required for replication, assembly etc., this is usually achieved by using viral producer cell lines capable of expressing one or more virus proteins. For example HEK293, Per.C6 and AGE1.HN cells express adenovirus E1A proteins and are, thus, capable of complementing DNA lacking E1 coding regions.
Fucosylation of molecules, e.g. proteins or lipids, comprising glycomoieties in eukaryotic cells (e.g. vertebrate cells) requires a nucleotide sugar, GDP-L-fucose, as a donor and also the presence of particular fucosyltransferases, which transfer the fucosyl residue from the donor to the acceptor molecule. In glycans from eukaryotic cells, e.g. vertebrate cells, fucose may be attached to the antennary GlcNAc via an alpha 1,3 linkage (terminal fucose) or to the asparagine-linked GlcNAc via an alpha 1,6 linkage (core fucose).
To achieve a homogenous, stable and site-directed attachment of the fucose analogue to the molecule such as protein, e.g. antibody, the attachment of a fucose analogue instead of a natural fucose via an alpha 1,6 linkage to the chitobiose core is preferred. Thus, the eukaryotic cell, e.g. vertebrate cell, of the present invention preferably comprises an enzymatically active alpha-1,6-fucosyltransferase. The (sole) presence of an enzymatically active alpha-1,6-fucosyltransferase is particularly preferred in the eukaryotic cell, e.g. vertebrate cell, of the present invention, if the production of fucose analogue coupled proteins is intended, which only comprise a 1,6 fucosylation site (e.g. natural, un-modified antibodies). This may further increase charge-homogeneity of the fucose analogue coupled to proteins via an alpha-1,6-fucosyltransferase N-glycosylation site.
Alternatively or additionally, the eukaryotic cell of the present invention preferably comprises an enzymatically active protein-O-fucosyltransferase. A protein-O-fucosyltransferase (P0FUT1) is an enzyme usually responsible for adding fucose sugars in O-linkage to serine or threonine residues. The protein is an inverting glycosyltransferase, which means that the enzyme uses GDP-β-L-fucose as a donor substrate and transfers the fucose in O-linkage to the protein producing fucose-α-O-serine/threonine. In the eukaryotic cell of the present invention, it can attach fucose analogues instead of natural fucose in O-linkage to serine or threonine residues comprised in the molecule structure. The (sole) presence of a protein-O-fucosyltransferase is particularly preferred in the eukaryotic cell, e.g. vertebrate cell, of the present invention, if the production of fucose analogue coupled proteins is intended which comprise one or more, e.g. 1, 2, 3, or 4, EGF-like repeat(s) comprising a serine and/or threonine residue(s), wherein said residue(s) is (are) recognized by said enzyme. This may further increases charge-homogeneity of the fucose analogue coupled proteins via a protein-O-fucosylation site.
In another preferred embodiment, the eukaryotic cell of the present invention does not comprise an enzymatically active alpha-1,3-fucosyltransferase. Preferably, the alpha-1,3-fucosyltransferase enzyme activity is abolished due to the overexpression, more preferably due to the constitutive and/or stable overexpression, of a suppressor of alpha-1,3-fucosylation such as histone deacetylase 5 (Hdac5). It is also preferred that the cell does not comprise an enzymatically active alpha-1,3-fucosyltransferase as (i) said enzyme is mutated so that it is not functionally active anymore, (ii) the gene encoding said enzyme is partially or fully knocked-out so that no functionally active enzyme is expressed, or (iii) the promoter region regulating the expression of the gene of said enzyme is partially or fully deleted so that no functionally active enzyme is expressed. Knock-down of the alpha-1,3-fucosyltransferase using miRNAs and/or siRNAs may also be possible.
The absence of an enzymatically active alpha-1,3-fucosyltransferase is particularly preferred in the eukaryotic cell, e.g. vertebrate cell, of the present invention, if the production of fucose analogue coupled proteins (e.g. antibodies) is intended which comprise artificial introduced N-glycosylation sites beside naturally occurring N-glycosylation sites (e.g. the artificial introduced N-glycosylation site(s) at amino acid position N276 and/or N159 and the naturally occurring N-glycosylation site at amino acid position N297 (numbered according to the Kabat system) in antibodies). While said artificial N-glycosylation sites may be accessible (due to the specific glycan structure at this position) by an alpha-1,3-fucosyltransferase and alpha-1,6-fucosyltransferase, the naturally occurring N-glycosylation sites may be accessible (due to the specific glycan structure at this position) by an alpha-1,6-fucosyltransferase. Thus, to allow the generation of molecule-pharmaceutically active compound-conjugates with high coupling stability and homogeneity, the (sole) presence of an enzymatically active alpha-1,6-fucosyltransferase and the absence of an enzymatically active alpha-1,3-fucosyltransferase is preferred.
The use of a eukaryotic cell of the present invention which is preferably devoid of alpha-1,3-fucosyltransferase activity results in sole remaining protein-O-fucosyltransferase and alpha-1,6-fucosyltransferase activity and, thus, leaves the protein-O-linked amino acid site and the alpha-1,6-linked core fucosylation site as the only sites to which a fucose analogue may be attached. This allows the generation of fucose analogue coupled proteins with high coupling stability and homogeneity, particularly the generation of antibodies which comprise both N-glycosylation sites which can be recognized by a alpha-1,6-fucosyltransferase and amino acid residues which can be recognized by a protein-O-fucosyltransferase.
It is preferred that the eukaryotic cell is a vertebrate cell. It is particularly preferred that the vertebrate cell is a mammalian, a fish, an amphibian, a reptilian cell or an avian cell.
It is more preferred that

    (i) the mammalian cell is a human, mouse, rat, hamster, canine or monkey cell, more particularly a Chinese hamster ovary (CHO) cell, a Syrian hamster fibroblast (BHK21) cell (ATCC CCL-10), a SP2/0-Ag14 cell (ATCC CRL-1581), a NS0 cell (ECACC No. 85110503), a human cervical carcinoma (HELA) cell (ATCC CCL 2), a human PER.C6 cell, or a human AGE1.HN cell,
    (ii) the fish cell is a Ictalurus punctatus (channel catfish) cell, more particularly a Ictalurus punctatus (channel catfish) ovary (CCO) cell (ATCC CRL-2772),
    (iii) the amphibian cell is a Xenopus laevis cell, more particularly a Xenopus laevis kidney cell (ATCC CCL-102),
    (iv) the reptilian cell is an Iguana iguana cell, more particularly an Iguana iguana heart (IgH-2) cell (ATCC CCL-108), or
    (v) the avian cell is an avian retina cell, more particularly a AGE1.CR.PIX cell, or an avian somite cell.


The cell line AGE1.CR.PIX was deposited with the DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany on Nov. 24, 2005 under accession number DSM ACC2749. The cell line AGE1.HN was deposited with the DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany on Nov. 4, 2005 under accession number DSM ACC2744.
As described above, it is particularly preferred that the cell is a Chinese hamster ovary (CHO) cell. CHO cells are cells which were originally isolated in 1952. Derivatives of parental lineage CHO pro-(specifically CHO-K1), which may be used herein, are CHO-S and CHO-SV cells. One variant of this lineage, DUKX B11, is modified to contain only one allele of the dhfr gene that is inactivated by mutation. Another CHO subline, DG44, diverges earlier from the common ancestor and lacks both alleles of dhfr (Urlaub et al., 1986, Proc Natl Acad Sci USA. 83 (2): 337-341). In most preferred embodiments of the present invention, the Chinese hamster ovary (CHO) cell is a CHO-K1 or CHO-DG44 cell.
CHO-K1 or CHO-DG44 cells are extensively applied in the production of recombinant proteins and antibodies. Despite the high flexibility of CHO cells in general, both CHO-K1 or CHO-DG44 cells have individual distinct features. CHO-K1 cells grow to higher peak cell densities, whereas DG44 cells usually show a higher specific productivity. Typically, media are not compatible between the two cell lineages. Preferred cell lines are summarized in the following Table 1:









TABLE 1






DEPOSITION



CELL LINE
NUMBER
ORIGIN







NS0
ECACC No. 85110503
Mouse Myeloma


Sp2/0-Ag14
ATCC CRL-1581
Mouse Myeloma


BHK21
ATCC CCL-10
Baby Hamster Kindney


HELA
ATCC CCL 2
Human cervical carcinoma


CHO
ECACC No. 8505302
Chinese Hamster Ovary


CHO wild-type
ECACC 00102307
Chinese Hamster Ovary


CHO-K1
ATCC CCL-61
Chinese Hamster Ovary


CHO-DUKX
ATCC CRL-9096
Chinese Hamster Ovary


(= CHO duk−,


CHO/dhfr−)


CHO-DUKX B11
ATCC CRL-9010
Chinese Hamster Ovary


CHO-DG44
not deposited at ATCC
Chinese Hamster Ovary



(Urlaub et al., 1983)


CHO Pro-5
ATCC CRL-1781
Chinese Hamster Ovary


CHO-S
Invitrogen Cat No.
Chinese Hamster Ovary



10743-029









As mentioned above, the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) is blocked in the eukaryotic cell, e.g. vertebrate cell, of the present invention. In preferred embodiments of the present invention, the GDP-L-fucose analogue comprised in said cell does not exert an inhibitory activity on said pathway in addition to a negative feedback inhibition that would be exerted by GDP-L-fucose. Thus, in preferred embodiments of the present invention, said GDP-L-fucose analogue does not efficiently inhibit said synthesis pathway. In more preferred embodiments of the present invention, the GDP-L-fucose analogue does not inhibit said synthesis pathway. It is even more preferred that the de novo pathway is not inhibited by the GDP-L-fucose analogue itself or by any other fucose analogue which is additionally present in said cell. Particularly, neither the GDP-L-fucose analogue (intracellular metabolized form) nor any other GDP-L-fucose analogue precursor (e.g. L-fucose analogue) inhibits the GDP-L-fucose synthesis pathway originating from GDP-D-mannose (de novo pathway) as describe above.
It is also preferred that the fucose analogue (in any form) is not an inhibitor of a fucosyltransferase (e.g. a 1,6-fucosyltransferase, 1,3-fucosyltransferase, and/or O-linked fucosyltransferase, preferably 1,6-fucosyltransferase such as FUT8 protein). Such an inhibition is not desired as it may abolish or reduce the incorporation of the fucose analogue into nascent glycostructures of the above-described molecules and/or its attachment to amino acids comprised in the above-described molecule.
The term “fucose analogue”, as used herein, is a compound which has a structure that allows, after incorporation of the L-fucose analogue into the glycomoieties of the molecule (e.g. protein, polypeptide, or lipid) mentioned above and/or after attachment of the L-fucose analogue to amino acids (amino acid recognition sites) comprised in the molecule (e.g. protein or polypeptide) mentioned above, the linkage of further pharmaceutically active compound to said molecule. The term “fucose analogue” preferably does not comprise any fucose molecule or fucose derivative that naturally occurs in eukaryotic cells.
It is preferred that the GDP-L-fucose analogue comprises one or more, e.g. 1, 2, 3, 4, 5, or 6, preferably 1 or 2, reactive and/or activated substitutions. Said one or more reactive and/or activated substitutions are suchlike that they allow, after incorporation of the L-fucose analogue into the glycomoieties of the molecule (e.g. protein, polypeptide, or lipid) mentioned above and/or after attachment of the L-fucose analogue to amino acids (amino acid recognition sites) comprised in the molecule (e.g. protein or polypeptide) mentioned above, the linkage of further pharmaceutically active compound to said molecule.
Preferably, fucose analogues including bioorthogonal fucose analogues or derivatives bear one or more functional group(s) for chemical coupling using different reactions including but not limited to ketoneaminooxy/hydrazide ligation (Mahal L K, Yarema K J, Bertozzi C R (1997) Science 276:1125-1128. Tai H C, Khidekel N, Ficarro S B, Peters E C, Hsieh-Wilson L C (2004) J Am Chem Soc 126:10500-10501.), Staudinger ligation (Saxon E, Bertozzi C R (2000) Science 287:2007-2010.), Michael addition (Sampathkumar S G, Li A V, Jones M B, Sun Z, Yarema K J (2006) Nat Chem Biol 2:149-152.), the Huisgen-Sharpless-Meldal Cu(I) catalyzed azide-alkyne cycloaddition (Click Chemistry, Huisgen, R. (1961). “Centenary Lecture-1,3-Dipolar Cycloadditions”. Proceedings of the Chemical Society of London: 357; H. C. Kolb, M. G. Finn and K. B. Sharpless (2001). “Click Chemistry: Diverse Chemical Function from a Few Good Reactions”. Angewandte Chemie International Edition 40 (11): 2004-2021, Tornoe, C. W.; Christensen, C.; Meldal, M. (2002). “Peptidotriazoles on Solid Phase: [1,2,3]-Triazoles by Regiospecific Copper(I)-Catalyzed 1,3-Dipolar Cycloadditions of Terminal Alkynes to Azides”. Journal of Organic Chemistry 67 (9): 3057-3064. Axford J S (1999) Biochim Biophys Acta 1455:219-229., Dube D H, Bertozzi CR (2005) Nat Rev Drug Discov 4:477-488. U.S. Pat. No. 7,375,234, Copper-catalysed ligation of azides and acetylenes), palladium-catalyzed Suzuki Cross Coupling, between organobornic acid and aryl or vinyl halides, pseudo-halides (including triflates), alkyls, alkenyls and/or alkynyls (Baxter, et al., J. Am. Chem. Soc, 2003, 125, 7198-7199; Wu, et ai, J. Org. Chem., 2003, 68, 670-673 and Molander, et al., J. Org. Chem., 2002, 67, 8424-8429), palladium-catalyzed Hiyama coupling of C—C bond formation between aryl, alkenyl, or alkyl halides or pseudohalides and organosilanes (Lee et al, J. Am. Chem. Soc., 2003, 125, 5616-5617; Denmark, et al., J. Am. Chem. Soc, 1999, 121, 5821-5822; Li, et al., Synthesis, 2005, 3039-3044; Murata, et ai, Synthesis, 2001, 2231-2233; Lee, Org. Lett, 2000, 2053-2055)., palladium or nickel catalyzed Kumada cross coupling of Grignard reagents with alkyl, vinyl or aryl halides (Frisch, et ai, Angew. Chem., 2002, 114, 4218-4221). nickel or palladium catalyzed Negishi Coupling of organozinc compounds with various halides (aryl, vinyl, benzyl or allyl) (Hadei, et ai, Org. Lett, 2005, 7, 3805-3807; Huo, et ai, Org. Lett., 2003, 5, 423-425; Lutzen, et ai, Eur. J. Org. Chem., 2002, 2292-2297), palladium-catalyzed Heck reaction C—C coupling between aryl halides or vinyl halides and activated alkenes in the presence of a base (Chandrasekhar, et al., Org. Lett., 2002, 4, 4399-4401; Masllorens, et al., Org. Lett, 2003, 5, 1559-1561; Battistuzzi, et al., Org. Lett, 2003, 5, 777-780; Mo, et al., J. Am. Chem. Soc, 2005, 127, 751-760; Hansen, et al., Org. Lett, 2005, 7, 5585-5587.), palladium-catalyzed Fukuyama Coupling of organozinc compounds with thioesters to form ketones (Tokuyama, et al., J. Braz. Chem. Soc, 1998, 9, 381-387), Sonogashira Coupling of terminal alkynes with aryl or vinyl halides using a palladium catalyst, a copper(l) cocatalyst, and an amine base (Liang, et al., J. Org. Chem., 2006, 71, 379-381; Gholap, et al., J. Org. Chem., 2005, 70, 4869-4872; Liang, et al., J. Org. Chem. 2005, 70, 391-393; Elangovan, et al., Org. Lett, 2003, 5, 1841-1844; Batey, et al., Org. Lett, 2002, 1411-1414)., copper(l) catalyzed Cadiot-Chodkiewicz coupling coupling of a terminal alkyne and an alkynl halide (Marino, et al., J. Org. Chem., 2002, 67, 6841-6844) and Eglinton, Glaser, or Hay reactions, (Gibtner, et al., Chem. Euro. J., 2002, 68, 408-432).
Preferably, the GDP-L-fucose analogue is synthesized from an L-fucose analogue. In preferred embodiments, the L-fucose analogue is added to the culture medium from which it is taken up by the eukaryotic cell of the present invention (e.g. by active transport or passive diffusion). The GDP-L-fucose analogue is then usually synthesized from an L-fucose analogue via the salvage pathway. It may also be possible to introduce a GDP-L-fucose analogue directly into the cell and, thus, to bypass the salvage pathway.
It is particularly preferred that the L-fucose analogue is a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose.
Other preferred fucose analogues are fucose analogues which comprise one or more, e.g. 1, 2, 3, 4, 5, or 6, preferably 1 or 2, of the chemical/functional group(s) indicated as chemical/functional group A or B in Table 2. Said chemical/functional groups allow chemical/functional coupling to the pharmaceutically active compound by any conjugation chemistry, e.g. by a conjugation chemistry as listed in Table 2.










TABLE 2





Chemical Coupling
Functional
Functional



Reaction
Group A
Group B
References







Ketoneaminooxy/
Ketoneaminooxy-
Hydrazide
Mahal LK, Yarema KJ, Bertozzi CR


Hydrazide Ligation
group

(1997) Science 276: 1125-1128.





Tai HC, Khidekel N, Ficarro SB,





Peters EC, Hsieh-Wilson LC





(2004) J Am Chem Soc





126: 10500-10501.


Staudinger Ligation
Azide
Phosphine or
Saxon E, Bertozzi CR (2000)




phosphit
Science 287: 2007-2010.


Michael Addition
α,β-unsaturated
Carbanion
Sampathkumar SG, Li AV, Jones



Carbonyl, Nitril
(deprotonated
MB, Sun Z, Yarema KJ (2006)



or Carbonic
Carbonyl)
Nat Chem Biol 2: 149-152.



Acid Amide


Huisgen-Sharpless-
Azide
Alkyne
Huisgen, R. (1961). “Centenary


Meldal Cu(I) catalyzed


Lecture - 1,3-Dipolar


azide-alkyne


Cycloadditions”. Proceedings of


cycloaddition


the Chemical Society of London:


(“Click Chemistry”)


357.





H. C. Kolb, M. G. Finn and K. B. Sharpless





(2001). “Click





Chemistry: Diverse Chemical





Function from a Few Good





Reactions”. Angewandte Chemie





International Edition 40 (11):





2004-2021.





Tornoe, C. W.; Christensen, C.;





Meldal, M. (2002).





“Peptidotriazoles on Solid Phase:





[1,2,3]-Triazoles by





Regiospecific Copper(I)-





Catalyzed 1,3-Dipolar





Cycloadditions of Terminal





Alkynes to Azides”. Journal of





Organic Chemistry 67 (9): 3057-3064.





Axford JS (1999) Biochim





Biophys Acta 1455: 219-229.





Dube DH, Bertozzi CR (2005)





Nat Rev Drug Discov 4: 477-488.





U.S. Pat. No. 7,375,234,





Copper-catalysed ligation of





azides and acetylenes.


Suzuki Cross Coupling
Organoboronic
Aryl or Vinyl
Baxter, et al., J. Am. Chem. Soc,


(palladium-catalyzed)
acid
Halides,
2003, 125, 7198-7199.




Pseudo-
Wu, et ai, J. Org. Chem., 2003,




Halides
68, 670-673.




(including
Molander, et al., J. Org. Chem.,




Triflates),
2002, 67, 8424-8429.




Alkyls,




Alkenyls




and/or




Alkynyls


Hiyama Coupling
aryl, alkenyl, or
organosilanes
Lee et al., J. Am. Chem. Soc.,


(palladium-catalyzed)
alkyl halides or

2003, 125, 5616-5617.



pseudohalides

Denmark, et al., J. Am. Chem.





Soc, 1999, 121, 5821-5822.





Li, et al., Synthesis, 2005, 3039-3044.





Murata, et al., Synthesis, 2001,





2231-2233.





Lee, Org. Lett, 2000, 2053-2055.


Kumada Cross
Grignard
Alkyl, Vinyl or
Frisch, et al., Angew. Chem.,


Coupling (palladium or
reagents
Aryl halides
2002, 114, 4218-4221.


nickel catalyzed)


Negishi Coupling
Organozinc
Aryl-, Vinyl-,
Hadei, et al., Org. Lett, 2005, 7,


(nickel or palladium
compound
Benzyl- or
3805-3807.


catalyzed)

Allyl-Halides
Huo, et al., Org. Lett., 2003, 5,





423-425.





Lutzen, et al., Eur. J. Org. Chem.,





2002, 2292-2297.


Heck reaction C-C
Aryl Halides or
Base activated
Chandrasekhar, et al., Org. Lett.,


coupling (palladium-
Vinyl Halides
Alkene
2002, 4, 4399-4401.


catalyzed)


Masllorens, et al., Org. Lett,





2003, 5, 1559-1561.





Battistuzzi, et al., Org. Lett, 2003,





5, 777-780.





Mo, et al., J. Am. Chem. Soc,





2005, 127, 751-760.





Hansen, et al., Org. Lett, 2005, 7,





5585-5587.


Fukuyama Coupling
Organozinc
Thioester
Tokuyama, et al., J. Braz. Chem.


(palladium-catalyzed)
compound

Soc, 1998, 9, 381-387.


Sonogashira Coupling
terminal Alkyne
Aryl or Vinyl
Liang, et al., J. Org. Chem., 2006,


(palladium catalyst,

Halide
71, 379-381.


copper(1) cocatalyst,


Gholap, et al., J. Org. Chem.,


and an amine base)


2005, 70, 4869-4872.





Liang, et al., J. Org. Chem. 2005,





70, 391-393.





Elangovan, et al., Org. Lett, 2003,





5, 1841-1844.





Batey, et al., Org. Lett, 2002,





1411-1414.


Cadiot-Chodkiewicz
terminal Alkyne
Alkynl halide
Marino, et al., J. Org. Chem.,


coupling (copper(1)


2002, 67, 6841-6844.


catalyzed)


Eglinton, Glaser, or
terminal Alkyne
terminal
Gibtner, et al., Chem. Euro. J.,


Hay reactions

Alkyne
2002, 68, 408-432.









It is preferred that only fucose analogues are selected for which the fucose kinase, the transporter and the fucosyltransferase are permissive.
The above mentioned chemical/functional groups may be attached at any C position in the fucose structure. However, a chemical/functional group attached at C-5 or C-6 is particularly preferred. The C-6 position is a methyl group in the native fucose molecule. In a preferred embodiment, the fucose analogue carries azido- or alkynyl-groups or metabolizable precursors of alkynyl- or azido-fucose analogues enabled for Huisgen Sharpless Meldal click chemistry.
In a second aspect, the present invention relates to a method for producing a molecule which comprises a fucose analogue comprising the steps of:

    (i) providing a eukaryotic cell according to the first aspect, and
    (ii) isolating the molecule comprising a fucose analogue from the cell in i).


Preferably, upon step i), the molecule which is capable of being a substrate for a fucosyltransferase, e.g. a protein or polypeptide, is expressed in the cell in i).
It is also preferred that the cell is cultured prior to the isolation of the molecule in step (ii). Culturing may be performed according to standard procedures readily available to the skilled person. It is particularly preferred that the eukaryotic cell is cultured prior to the isolation of the molecule in step (ii) in a cell culture medium devoid of natural fucose or a metabolizable precursor of natural fucose. Instead of natural fucose or a metabolizable precursor of natural fucose, an effective amount of a fucose analogue is added to the culture medium. In this context, the term “effective amount” refers to an amount of the analogue which is sufficient so that the fucose analogue is incorporated into nascent glycostructures and/or added to amino acids. The amount of the fucose analogue that is effective can be determined by standard cell culture methodologies (see examples). For example, cell culture assays may be employed to help to identify optimal dosage ranges. The precise amount to be employed also depends on the time of administration, the cell type used, the cell density and the like. Effective doses may be extrapolated from dose-response curves derived form in vitro model test systems. In addition, the skilled person is able to analyse the molecule structure of the molecule produced with the method of the second aspect of the present invention in order to determine the presence of fucose analogues attached to or incorporated into said molecule structure. As an example, MALDI-TOF/TOF could be used (see also the methods indicated above). Other methods to determine the molecule structure, particularly the sugar structure, include hydazinolysis or enzyme digestion. In some embodiments, the fucose analogue is present in the culture medium at a concentration of between 0.1 nM to 50 mM or of between 10 nM to 50 mM, preferably of between 10 nM to 10 mM, more preferably of between 100 nM to 5 mM, 100 nM to 3 mM, or 100 nM to 2 mM, e.g. 10 nM, 20 nM, 30 nM, 40 nM, 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, 150 nM, 160 nM, 170 nM, 180 nM, 190 nM, 200 nM, 250 nM, 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 600 nM, 700 nM, 800 nM, 900 nM, 1 mM, 1.5 mM, 2 mM, 2.5 mM, 3 mM, 3.5 mM, 4 mM, 4.5 mM, 5 mM, 10 mM, 20 mM, 30 mM, 40 mM, or 50 mM.
The molecule, e.g. protein, polypeptide, or lipid, comprising a fucose analogue on its glycomoieties and/or amino acids can be readily isolated in step ii) from the eukaryotic cell, e.g. vertebrate cell. Various isolation procedures are known in the art for molecules enclosed inside eukaryotic cells (e.g. vertebrate cells) or secreted from such cells comprising the modified molecules. Such methods typically involve cell harvest, disintegration and fractionation/purification in the case of intracellular molecules and generation of a cell free culture supernatant followed by purification of secreted molecules.
An extraction procedure that is useful according to the invention does not interfere with modified molecules to be isolated. For example, extraction is preferably performed in the absence of strong detergents and reducing agents, or any agent that may induce protein denaturation.
It will be understood by a skilled person that the molecule, e.g. protein, polypeptide, or lipid, which comprises a fucose analogue, e.g. on its glycomoieties and/or amino acids, produced in the method of the second aspect of the present invention is a glycomolecule, e.g. a glycoprotein, glycopolypeptide, or glycolipid.
In a third aspect, the present invention relates to a molecule comprising a fucose analogue obtainable by the method of the second aspect. Said molecule is a molecule as set out above with respect to the first aspect and said fucose analogue is a fucose analogue as set out above with respect to the first aspect. Preferably, said fucose analogue comprises one or more, e.g. 1, 2, 3, 4, 5, or 6, preferably 1, or 2, reactive or activated substitutions for binding a pharmaceutically active compound. Preferred fucose analogues are fucose analogues which comprise one or more, e.g. 1, 2, 3, 4, 5, or 6, preferably 1 or 2, of the chemical/functional group(s) indicated as chemical/functional group A or B in Table 2. Said chemical/functional groups allow chemical/functional coupling/binding to the pharmaceutically active compound by any conjugation chemistry, e.g. by a conjugation chemistry as listed in Table 2 (see also first aspect). It is particularly preferred that the protein or polypeptide is an antigen binding protein or polypeptide, preferably an antibody, an antibody fragment, a virus protein, a virus protein fragment, a hormone, or an antigen. It is also particularly preferred that the lipid is a glyceroglycolipid, most preferably a galactolipid, a sulfolipid (SQDG), or a glycosphingolipids, most preferably a cerebroside (e.g. a galactocerebroside or a glucocerebroside), a ganglioside, a globoside, a sulfatide or a glycophosphosphingolipid. Preferably, the lipid, e.g. ganglioside, is comprised in the membrane of an enveloped virus. Most preferably, the virus protein and/or lipid are comprised in the envelope of an enveloped virus (see also first aspect).
In a further aspect, the present invention provides a composition of molecules according to the third aspect. In said composition, the molecules according to the third aspect comprise preferably to 50%, more preferably to 60% or 70%, even more preferably to 80% or 90%, and most preferably to 95% or 100%, e.g. to 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99%, or 100%, a fucose analogue attached to its glycomoieties and/or amino acids. It is particularly preferred that the molecules according to the third aspect comprise an identical number of fucose analogues attached to its glycomoieties and/or amino acids, e.g. 1, 2, 3, 4, 5, 6, 7, or 8 fucose analogues.
In a fourth aspect, the present invention relates to a method for producing a conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound comprising the steps of:

    (i) carrying out the method of the second aspect, and
    (ii) covalently coupling a pharmaceutically active compound via the fucose analogue to the molecule comprising said fucose analogue.


Said molecule is a molecule as set out above with respect to the first aspect and said fucose analogue is a fucose analogue as set out above with respect to the first aspect.
The term “pharmaceutically active compound”, as used herein, refers to any compound being pharmaceutically useful or having a pharmaceutical effect. Preferably, said compound contains one or more, e.g. 1, 2, 3, 5, or 6, preferably 1 or 2, chemical/functional group(s), e.g. one or more of the chemical/functional group(s) indicated as chemical/functional group A or B in Table 2, that allow(s) chemical/functional coupling to the fucose analogue by any conjugation chemistry, e.g. by a conjugation chemistries as listed in Table 2. It should be noted that if a chemical/functional group as indicated as chemical/functional group A has been chosen for the pharmaceutically active compound, the respective chemical/functional group as indicated as chemical/functional group B has to be chosen for the fucose analogue in order to allow efficient and successful coupling of a pharmaceutically active compound via the fucose analogue to the molecule comprising said fucose analogue. In turn, if a chemical/functional group as indicated as chemical/functional group B has been chosen for the pharmaceutically active compound, the respective chemical/functional group as indicated as chemical/functional group A has to be chosen for the fucose analogue in order to allow efficient and successful coupling of a pharmaceutically active compound via the fucose analogue to the molecule comprising said fucose analogue.
Preferably, the pharmaceutically active compound contains an alkynyl- or azido-group that allows functional coupling to the alkynyl- or azido-modified fucose analogue incorporated into the protein-linked glycostructure or attached to the amino acid sequence. The pharmaceutically active compound may be a cytotoxic drug intended for therapy against tumors or chronic infectious diseases, including but not limited to compounds which are 100 to 1000 fold more toxic than the classical chemotherapeutic drugs. Such compounds include but are not limited to the extremely toxic calicheamicin and caliceamicin derivatives, auristatin or auristatin derivatives, maytansin, maytansin derivatives or maytansinoids such as DM1 and the very toxic DNA intercalating anthracycline antibiotics, doxorubicin, daunorubicin, epirubicin, esorubicin and idarubicin. Moreover, the pharmaceutically active compounds may include but are not limited to vinca alkaloids such as vincristin, vinblastin, vindesin, vinorelbin, taxanes such as paclitaxel, docetaxel, toxalbumins such as ricin, abrin, modeccin, viscumin, volkensin, topoisomerase inhibitors such as etoposid, teniposid, irinotecan, topotecan, actinomycines such as actinomycin D, dactinomycin, mitoxanthrone, amsacrin, and other extremely poisonous compounds such as phalloidin, alpha-amanitin, alflatoxin, dolastatin, methothrexate, miltefosin, imatinib and enzymatically active asparaginases and RNAses such as Barnase, Onconase, angiogenin ribonuclease, human pancreatic RNase, bovine seminal RNase, and eosinophil derived neurotoxin (EDN). The pharmaceutically active compound can also be a pharmacokinetic half life extender including but not limited to artificial synthetic polysialylated oligosaccharides, polyethylenglycol (PEG), homo-amino acid polymer (HAP), hydroxyethylstarch (HES) and albumin. The pharmaceutically active compound can also be an adjuvant including but not limited to β-glucans, squalenes, block copolymer (titermax), cytokines, diterpene alcohols, preferably a phytol, bacterial monophosphoryl lipid A, trehalose dicorynomycolate, rhamnose and rhamnose containing oligosaccharides, saponines, Toll-like receptor agonists such as LPS, lipoproteins, lipopeptides, flagellin, double-stranded RNA, unmethylated CpG islands, U-rich single strand RNA, imiquimod, haemaglutinin. From the above mentioned toxins, fragments could be used. Toxins or toxin fragments as pharmaceutically active compounds are particularly preferred.
In a fifth aspect, the present invention relates to a conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound obtainable by the method of the fourth aspect.
In a further aspect, the present invention provides a composition of conjugates comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound according to the fifth aspect. In said composition, the conjugates according to the fifth aspect comprise preferably to 50%, more preferably to 60% or 70%, even more preferably to 80% or 90%, and most preferably to 95% or 100%, e.g. to 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99%, or 100%, a fucose analogue attached to its glycomoieties and/or amino acids and a pharmaceutically active compound attached to said fucose analogue. It is particularly preferred that the conjugates according to the fifth aspect comprise an identical number of fucose analogues attached to its glycomoieties and/or amino acids, e.g. 1, 2, 3, 4, 5, 6, 7, or 8 fucose analogues, to which a pharmaceutically active compound is conjugated.
In a sixth aspect, the present invention relates to a conjugate which comprises a protein or polypeptide comprising one or more of the following structures:

—NG-cF*—Yo—C,

wherein each is attached to an N-glycosylation site comprised in said protein or polypeptide,

NG is an N-linked glycomoiety of said protein or polypeptide,

cF* is a core fucose analogue,

Y is a spacer unit, wherein o is an integer of 0 or 1, and

C is a pharmaceutically active compound.

The spacer unit Y may be absent (o=0) or present (o=1). Suitable spacer units such amino acid linker are known to the person skilled in the art. It will be clear for the person skilled in the art that the expression “-” in the conjugates described herein refers to a “covalent bond.
The protein or polypeptide is preferably a protein or polypeptide as described with respect to the first aspect of the present invention, the fucose analogue is preferably a fucose analogue as described with respect to the first aspect of the present invention and/or the pharmaceutically active compound is preferably a pharmaceutically active compound as described with respect to the fourth aspect of the present invention. Further, the protein comprising a fucose analogue may be a protein according to the third aspect of the present invention, or the conjugate may be a conjugate comprising a molecule comprising a fucose analogue and a pharmaceutically active compound according to the fifth aspect of the present invention.
In a preferred embodiment, the conjugate comprises a protein or polypeptide comprising between 1 to 8, preferably 1 to 6, more preferably 1 to 3, e.g. 1, 2, 3, 4, 5, 6, 7, or 8, of the following structures: —NG-cF*—Yo—C,
wherein each is attached to an N-glycosylation site comprised in said protein or polypeptide.
Preferably, the glycomoiety is an N-linked glycomoiety of the complex type, more preferably the N-linked glycomoiety of the complex type has the glycostructure G0F*, G0F*-GlcNAc, G1F* or G2F* (see above structure definitions).
It is preferred that the polypeptide which is comprised in the conjugate is an antibody fragment, e.g. an antibody fragment as described with respect to the first aspect of the present invention. It is particularly preferred that the polypeptide which is comprised in the conjugate is an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain).
It is more preferred that the conjugate comprises an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain), comprising one or more, e.g. 1, 2, or 3, of the following structures: —NG-cF*—Yo—C,
wherein each is attached to an N-glycosylation site selected from the group consisting of asparagine N297, asparagine N159, and asparagine N276 (numbered according to the Kabat numbering system) comprised in said antibody heavy chain (H), preferably constant domain of said heavy chain (CH domain).
Thus, in a most preferred embodiment,

    (i) one —NG-cF*—Yo—C structure is attached to the N-glycosylation site at asparagine N297, asparagine N159, or asparagine N276 comprised in said antibody heavy chain, preferably constant domain of said heavy chain, or
    (ii) one —NG-cF*—Yo—C structure is attached to the N-glycosylation site at asparagine N297, one —NG-cF*—Yo—C structure is attached to the N-glycosylation site at asparagine N159, and/or one —NG-cF*—Yo—C structure is attached to the N-glycosylation site at asparagine N276 (all numbered according to the Kabat numbering system) comprised in said antibody heavy chain, preferably constant domain of said heavy chain.


The N-glycosylation site at asparagine N159 is particularly generated due to the replacement of G161 by S161 and the N-glycosylation site at asparagine N276 is particularly generated due to the replacement of Y278 by S278 (all numbered according to the Kabat numbering system). Thus, the above-mentioned antibody heavy chain (H), particularly the constant domain of a heavy chain (CH domain), comprised in the conjugate, preferably further comprises the point mutations G161→S161 (G161 replaced by S161) and/or Y278→S278 (Y278 replaced by S278) (all numbered according to the Kabat numbering system).
More preferably, the antibody heavy chain constant domain has an amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein the amino acids G161 (CH) and/or Y278 (CH) (numbered according to the Kabat numbering system) are substituted with serine. Also preferred are variants, particularly functionally active variants, of said sequences. As to the further characterization of said variants, it is referred to the first aspect of the present invention.
In the more and most preferred embodiments mentioned above, the fucose analogue is preferably a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose, and the pharmaceutically active compound is preferably a toxin or a toxin fragment.
In a preferred embodiment, the conjugate comprises 1, 2, or 3 cF*-linked pharmaceutically active compounds.
Preferably, the protein or polypeptide, e.g. antibody fragment such as an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain), comprised in the above-mentioned conjugate further comprises one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats comprising a serine and/or threonine residue to which the following structure:

—F*—Yp—C

is attached, wherein

F* is a fucose analogue moiety directly linked to said serine and/or threonine residue,

Y is a spacer unit, wherein p is an integer of 0 or 1, and

C is a pharmaceutically active compound.

The spacer unit Y may be absent (p=0) or present (p=1). Suitable spacer units such amino acid linker are known to the person skilled in the art. As to the preferred fucose analogues, it is referred to the first aspect of the present invention and as to the preferred pharmaceutically active compounds it is referred to the fourth aspect of the present invention. As specified in the more and most preferred embodiments mentioned above, the fucose analogue is preferably a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose, and the pharmaceutically active compound is preferably a toxin or a toxin fragment.
As to the definition/description of the EGF-like repeat, it is also referred to the first aspect of the present invention. Said EGF-like repeats may be located within the amino acid sequence of said protein or polypeptide or may be comprised at the N-terminus and/or C-terminus of said protein or polypeptide. Preferably, said EGF-like repeat is comprised at the C-terminus and/or N-terminus of the protein or polypeptide, e.g. antibody fragment such as an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain). More preferably, said EGF-like repeat is an EGF-like repeat with an amino acid sequence according to SEQ ID NO: 10 or a variant thereof which is at least 80% or 85%, more preferably 90% or 95%, most preferably 98% or 99%, e.g. 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 95, 96, 97, 98, or 99%, identical to said amino acid sequence. As to the further characterization of a variant of SEQ ID NO: 10, it is also referred to the first aspect of the present invention.
In a preferred embodiment, the conjugate comprises 1, 2, or 3 cF*-linked pharmaceutically active compounds and 1 or 2 F*-linked pharmaceutically active compounds.
The antibody heavy chain (CH), preferably the constant domain of a heavy chain (CH domain may also be comprised in a polypeptide to which the EGF-like repeat (e.g. SEQ ID NO: 10) is N-terminally and/or C-terminally added.
In a further aspect, the present invention relates to an antibody comprising two conjugates as defined in the sixth aspect. Said conjugates may comprise an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain), as defined above.
In a preferred embodiment, the antibody comprises two conjugates each comprising 1, 2, 3, or 4 cF*-linked pharmaceutically active compounds and preferably 1 or 2 F*-linked pharmaceutically active compounds.
In a seventh aspect, the present invention relates to a conjugate which comprises a protein or polypeptide comprising one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats comprising a serine and/or threonine residue to which the following structure:

—F*—Yp—C

is attached, wherein

F* is a fucose analogue moiety directly linked to said serine and/or threonine residue,

Y is a spacer unit, wherein p is an integer of 0 or 1, and

C is a pharmaceutically active compound.

The spacer unit Y may be absent (p=0) or present (p=1). Suitable spacer units such amino acid linker are known to the person skilled in the art.
The protein or polypeptide is preferably a protein or polypeptide as described with respect to the first aspect of the present invention, the fucose analogue is preferably a fucose analogue as described with respect to the first aspect of the present invention and/or the pharmaceutically active compound is preferably a pharmaceutically active compound as described with respect to the fourth aspect of the present invention. Further, the protein comprising a fucose analogue may be a protein according to the third aspect of the present invention, or the conjugate may be a conjugate comprising a molecule comprising a fucose analogue and a pharmaceutically active compound according to the fifth aspect of the present invention.
It is preferred that the polypeptide which is comprised in the conjugate is an antibody fragment, e.g. an antibody fragment as described with respect to the first aspect of the present invention. It is particularly preferred that the polypeptide which is comprised in the conjugate is an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain).
It is further preferred that the fucose analogue is a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose, and that the pharmaceutically active compound is a toxin or a toxin fragment.
As to the definition/description of the EGF-like repeat, it is also referred to the first aspect of the present invention. Said EGF-like repeats may be located within the amino acid sequence of said protein or polypeptide or may be comprised at the N-terminus and/or C-terminus of said protein or polypeptide. Preferably, said EGF-like repeat is comprised at the C-terminus and/or N-terminus of the protein or polypeptide, e.g. antibody fragment such as an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain). More preferably, said EGF-like repeat is an EGF-like repeat with an amino acid sequence according to SEQ ID NO: 10 or a variant thereof which is at least 80% or 85%, more preferably 90% or 95%, most preferably 98% or 99%, e.g. 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 95, 96, 97, 98, or 99%, identical to said amino acid sequence. As to the further characterization of a variant of SEQ ID NO: 10, it is also referred to the first aspect of the present invention.
In a preferred embodiment, the conjugate comprises 1, 2, 3, or 4, preferably 1 or 2, F*-linked pharmaceutically active compounds.
The antibody heavy chain (CH), preferably the constant domain of a heavy chain (CH domain may also be comprised in a polypeptide to which the EGF-like repeat (e.g. SEQ ID NO: 10) is N-terminally and/or C-terminally added.
In a further aspect, the present invention relates to an antibody comprising two conjugates as defined in the seventh aspect. Said conjugates may comprise an antibody heavy chain (H), preferably the constant domain of a heavy chain (CH domain), as defined above.
In a preferred embodiment, the antibody comprises two conjugates each comprising 1, 2, 3, or 4, preferably 1 or 2, F*-linked pharmaceutically active compounds.
In the above-mentioned conjugates, the pharmaceutically active compound is linked to the protein backbone at a given site by a homogenous glycostructure or sub-glycostructure—a homogenous glycostructure being an O-linked fucose residue directly linked to an amino acid side chain of the protein backbone, a homogenous sub-glycostructure being the two proximal sugar-residues of the N-linked chitobiose core of a complex N-glycan, i.e. the asparagine-linked N-acetylglucosamine and its alpha-1,6-linked core-fucose residue. Compared to undefined protein—conjugates where the functional compound is coupled via other terminal sugars of a microheterogeneous glycostructure, such defined and homogenous fucose-linked conjugates as described herein offer the practical benefit of enhanced lot consistency, easier analytics for product comparability and coupling efficiency and a more predictable stability profile.
In an eighth aspect, the present invention relates to a pharmaceutical composition comprising

    (i) the conjugate according to the sixth aspect or a pharmaceutically acceptable salt thereof, or
    (ii) the antibody comprising two conjugates according to the sixth aspect or a pharmaceutical acceptable salt thereof.


In a ninth aspect, the present invention relates to a pharmaceutical composition comprising

    (i) the conjugate according to the seventh aspect or a pharmaceutically acceptable salt thereof, or
    (ii) the antibody comprising two conjugates according to the seventh aspect or a pharmaceutically acceptable salt thereof.


The term “pharmaceutically acceptable salt” refers to a salt of a compound identifiable by the methods of the present invention or a compound of the present invention. Suitable pharmaceutically acceptable salts include acid addition salts which may, for example, be formed by mixing a solution of compounds of the present invention with a solution of a pharmaceutically acceptable acid such as hydrochloric acid, sulfuric acid, fumaric acid, maleic acid, succinic acid, acetic acid, benzoic acid, citric acid, tartaric acid, carbonic acid or phosphoric acid. Furthermore, where the compound carries an acidic moiety, suitable pharmaceutically acceptable salts thereof may include alkali metal salts (e.g., sodium or potassium salts); alkaline earth metal salts (e.g., calcium or magnesium salts); and salts formed with suitable organic ligands (e.g., ammonium, quaternary ammonium and amine cations formed using counteranions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl sulfonate and aryl sulfonate). Illustrative examples of pharmaceutically acceptable salts include, but are not limited to, acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bicarbonate, bisulfate, bitartrate, borate, bromide, butyrate, calcium edetate, camphorate, camphorsulfonate, camsylate, carbonate, chloride, citrate, clavulanate, cyclopentanepropionate, digluconate, dihydrochloride, dodecylsulfate, edetate, edisylate, estolate, esylate, ethanesulfonate, formate, fumarate, gluceptate, glucoheptonate, gluconate, glutamate, glycerophosphate, glycolylarsanilate, hemisulfate, heptanoate, hexanoate, hexylresorcinate, hydrabamine, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, hydroxynaphthoate, iodide, isothionate, lactate, lactobionate, laurate, lauryl sulfate, malate, maleate, malonate, mandelate, mesylate, methanesulfonate, methylsulfate, mucate, 2-naphthalenesulfonate, napsylate, nicotinate, nitrate, N-methylglucamine ammonium salt, oleate, oxalate, pamoate (embonate), palmitate, pantothenate, pectinate, persulfate, 3-phenylpropionate, phosphate/diphosphate, picrate, pivalate, polygalacturonate, propionate, salicylate, stearate, sulfate, subacetate, succinate, tannate, tartrate, teoclate, tosylate, triethiodide, undecanoate, valerate, and the like (see, for example, S. M. Berge et al., “Pharmaceutical Salts”, J. Pharm. Sci. 66:1-19 (1977)).
Preferably, the pharmaceutical composition further comprises one or more pharmaceutically acceptable excipient(s) and/or carrier(s).
The term “pharmaceutically acceptable excipient” when used herein is intended to indicate all substances in a pharmaceutical formulation which are not active ingredients such as, e.g., carriers, binders, lubricants, thickeners, surface active agents, preservatives, emulsifiers, buffers, flavoring agents, or colorants.
The term “pharmaceutically acceptable carrier” includes, for example, magnesium carbonate, magnesium stearate, talc, sugar, lactose, pectin, dextrin, starch, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose, a low melting wax, cocoa butter, and the like.
The pharmaceutical compositions of the present invention may be formulated in various ways well known to one of skill in the art and as described above.
The pharmaceutical compositions are preferably in unit dosage form. In such form the preparation is subdivided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Also, the unit dosage form can be a capsule, tablet, cachet, or lozenge itself, or it can be the appropriate number of any of these in packaged form.
In a tenth aspect, the present invention relates to

    (i) a conjugate according to the sixth aspect, an antibody comprising two conjugates according to the sixth aspect, or a pharmaceutical composition according to the eight aspect, or
    (ii) a conjugate according to the seventh aspect, an antibody comprising two conjugates according to the seventh aspect, or a pharmaceutical composition according to the ninth aspect


for treating, ameliorating, or preventing cancer or diseases caused by infections.
The treatment of cancer may involve the killing or inhibiting the proliferation of cancer/tumor cells and/or the infections may be viral or bacterial infections. Therefore, it is particularly preferred that the pharmaceutically active compound comprised in said conjugates is a toxin or a toxin fragment (see above). Such treatment, for example, involves the administration of an amount of the conjugate or antibody effective to kill or inhibit the proliferation of the tumor cells, cancer cells, immune cells or infected cells. The dosages, however, may be varied depending upon the requirements of the patient, the severity of the condition being treated, and the compound being employed. For treating, ameliorating, or preventing said conditions, the conjugates, antibodies or pharmaceutical compositions of the present invention can be administered to an animal patient, preferably a mammalian patient, preferably a human patient, orally, buccally, sublingually, intranasally, via pulmonary routes such as by inhalation, via rectal routes, or parenterally, for example, intracavernosally, intravenously, intra-arterially, intraperitoneally, intrathecally, intraventricularly, intraurethrally intrasternally, intracranially, intramuscularly, or subcutaneously.
In an eleventh aspect, the present invention provides a polypeptide comprising an antibody heavy chain constant domain (CH domain) comprising an N-glycosylation site at asparagine N276, particularly generated due to the replacement of Y278 by S278 (Y278→S278), and/or an N-glycosylation site at asparagine N159, particularly generated due to the replacement of G161 by S161 (G161→S161) (all numbered according to the Kabat numbering system).
Preferably, the above mentioned polypeptide further comprises 1 or 2 of the following structures —NG-cF*
attached to the N-glycosylation sites asparagine N276 and/or asparagine N159 comprised in said antibody heavy chain constant domain (CH domain), wherein
NG is an N-linked glycomoiety of said antibody, and
cF* is a core fucose analogue.
The fucose analogue may be a fucose analogue as described with respect to the first aspect of the invention. It is particularly preferred that the fucose analogue is a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose.
The antibody heavy chain constant domain comprised in said polypeptide may further comprise an (naturally) N-glycosylation site at asparagine N297. To this N-glycosylation site the above-mentioned structure —NG-cF* may further be attached.
Preferably, the above-described antibody heavy chain constant domain comprised in said polypeptide has an amino acid sequence according to SEQ ID NO: 8 or SEQ ID NO: 9, wherein the amino acids G161 (CH) and/or Y278 (CH) (numbered according to the Kabat numbering system) are substituted with serine. Also encompassed are variants, particularly functionally active variants, of said sequences (see first aspect of the invention).
The above-described polypeptide may further comprise one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats comprising a serine and/or threonine residue. Said EGF-like repeats may have an amino acid sequence according to SEQ ID NO: 10. Also encompassed are variants of SEQ ID NO: 10 (see first aspect of the invention). Said EGF-like repeat (e.g. SEQ ID NO: 10) may be comprised at the N-terminus and/or C-terminus of said polypeptide.
To said serine and/or threonine residue comprised in the one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats, the following structure: —F*
may further be added, wherein F* is a fucose analogue moiety directly linked to said serine and/or threonine residue comprised in said EGF-like repeat(s).
In a further aspect, the present invention provides an antibody comprising two of the polypeptides as defined in the eleventh aspect, preferably an antibody comprising two of the fucose analogue comprising polypeptides as defined in the eleventh aspect. Such an antibody (without EGF-like repeats) may enable, for example, the synthesis of defined (immuno)conjugates having 2 to 6 pharmaceutically active compounds covalently linked per antibody molecule (1 to 3 per CH domain comprised in each polypeptide), or such an antibody (with EGF-like repeats) may enable, for example, the synthesis of defined (immuno)conjugates having 3 to 10 pharmaceutically active compounds covalently linked per antibody molecule (1 to 3 per CH domain comprised in each polypeptide and 1 or 2 EGF-like repeats attached to the N-terminus and/or C-terminus of each polypeptide).
In a twelfth aspect, the present invention provides a polypeptide comprising one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats comprising a serine and/or threonine residue. Said EGF-like repeats may have an amino acid sequence according to SEQ ID NO: 10. Also encompassed are variants of SEQ ID NO: 10 (see first aspect of the invention). Said EGF-like repeat (e.g. SEQ ID NO: 10) may be comprised at the N-terminus and/or C-terminus of said polypeptide. As to the definition of the EGF-like repeats it is referred to the first aspect of the present invention. Said EGF-like repeats are preferably repeats which are naturally not comprised in said polypeptide, thus, artificial EGF-like repeats.
To said serine and/or threonine residue comprised in the one or more, e.g. 1, 2, 3, or 4, preferably 1 or 2, EGF-like repeats, the following structure: —F*
is preferably further added, wherein F* is a fucose analogue moiety directly linked to said serine and/or threonine residue comprised in said EGF-like repeat(s).
The fucose analogue may be a fucose analogue as described with respect to the first aspect of the invention. It is particularly preferred that the fucose analogue is a peracetylated fucose analogue, preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-fucose, more preferably a pyranosyl form of 1,2,3,4-tetraacetyl-azido-6-fucose.
In a further aspect, the present invention provides an antibody comprising two of the polypeptides as defined in the twelfth aspect, preferably an antibody comprising two of the fucose analogue comprising polypeptides as defined in the twelfth aspect.
In a thirteenth aspect, the present invention relates to a pharmaceutical composition comprising

    (i) the polypeptide according to the eleventh aspect or a pharmaceutically acceptable salt thereof, or the polypeptide according to the twelfth aspect or a pharmaceutically acceptable salt thereof, or
    (ii) the antibody comprising two polypeptides according to the eleventh aspect or a pharmaceutical acceptable salt thereof, or the antibody comprising two polypeptides according to the twelfth aspect or a pharmaceutically acceptable salt thereof.


Preferably, the pharmaceutical composition further comprises one or more pharmaceutically acceptable excipient(s) and/or carrier(s). As to the definition of the term “pharmaceutically acceptable salt”, it is referred to the above. Preferred pharmaceutically acceptable excipient(s) and/or carrier(s) are also described above.
In another further aspect, the present invention relates to methods for diagnosing an autoimmune disease, an infectious disease or cancer in a patient by administering an effective amount of immunoconjugate that binds to an antigen associated with the autoimmune disease, and detecting the immunoconjugate in the patient. In yet another aspect, a virus or vaccine antigen, decorated with the fucose analogue by having said virus or vaccine antigen being produced by the engineered cell of the present invention, can be linked to a conjugate that serves as vaccine adjuvant (such as squalene or CpG DNA), or that helps to target the vaccine antigen to antigen-presenting cells (for example, by linkage to a ligand for toll-like receptors), or that interferes with infectivity to support attenuation (weakening) of the thus treated virus (for example by inducing crosslinkage with doubly functionalized conjugates), or that labels the virus with a dye such as ALEXA or FITC to allow visualization of the infection in tissue culture or living organism.
In a further aspect, the present invention relates to a kit of parts comprising a eukaryotic cell for producing a molecule comprising a fucose analogue, wherein in said cell the GDP-L-fucose synthesis pathway originating from GDP-D mannose is blocked and a GDP-fucose analogue. In another further aspect, the present invention relates to a cell culture system comprising a eukaryotic cell for producing a molecule comprising a fucose analogue, wherein in said cell the GDP-L-fucose synthesis pathway originating from GDP-D mannose is blocked and comprising a fucose analogue in the cell culture medium. All terms used in the description of these aspects have meaning as described above.
Various modifications and variations of the invention will be apparent to those skilled in the art without departing from the scope of invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in the art in the relevant fields are intended to be covered by the present invention.
Some of the amino acid sequences described herein are summarized as follows:









SEQ ID NO: 8



(IgG1 CH Allele 01, human)



ASTKGPSVFP LAPSSKSTSG GTAALGCLVK



 



DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT



 



VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP



 



PCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVS



 



HEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLT



 



VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ



 



VYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQP



 



ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV



 



MHEALHNHYT QKSLSLSPGK



 



SEQ ID NO: 9



(IgG1 CH Allele 02, human)



ASTKGPSVFP LAPSSKSTSG GTAALGCLVK



 



DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT



 



VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP



 



PCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVS



 



HEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLT



 



VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ



 



VYTLPPSREE MTKNQVSLTC LVKGFYPSDI AVEWESNGQP



 



ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV



 



MHEALHNHYT QKSLSLSPGK



 



SEQ ID NO: 10



(EGF-like repeat)



DGDGCASSPCQNGGSCKDQLQSYIC






The following figures and examples are merely illustrative of the present invention and should not be construed to limit the scope of the invention as indicated by the appended claims in any way.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows an overview of the fucose salvage and de novo pathways in eukaryotic cells (e.g. vertrebrate cells). In the absence of fucose, cells are unable to synthesize GDP-fucose via the salvage pathway (see right hand panel). The de novo pathway can be blocked by enzymatic conversion of the intermediate GDP-4-keto-6-deoxymannose into a dead end product that typically does not occur in vertebrate cells (left hand panel). If the deflecting enzyme is RMD, for example, then the dead end product is GDP-D-rhamnose. GDP-deoxyhexoses such as GDP-D-rhamnose may exert a feedback inhibition on the GMD-enzyme thereby further blocking the fucose de novo pathway as well as the alternate GDP-rhamnose synthesis.
FIG. 2 shows GFP-fluorescence of RMD-CHO-IgG cells that stably overexpress the RMD transgene.
FIG. 3 shows a RT-PCR analysis of clones expressing the RMD-Transgene. Lane M=bp-DNA-Marker, Lane 1: RMD-CHO-IgG clone 1; Lane 2: RMD-CHO-IgG clone 2; Lane 3: RMD-CHO-IgG clone 3; Lane 4: RMD-CHO-IgG clone 4; Lane 5: RMD-CHO-IgG clone 5; Lane 6: RMD-CHO-IgG clone 6; Lane 7: CHO-IgG parental clone; Lane 8: negative PCR control. The RMD band is visible in all RMD-transfected clones.
FIG. 4 shows the determination of the minimum required fucose analogue concentration to achieve restoration of the core-fucosylation status of antibodies secreted from an RMD-modified cell line.



REFERENCES


    Campbell, C. and Stanley, P. (1983) Regulatory mutations in CHO cells induce expression of the mouse embryonic antigen SSEA-1. Cell, 35, 303-309.
    Chen, W., Tang, J., Stanley, P. Suppressors of α(1,3)fucosylation identified by expression cloning in the LEC11B gain-of-function CHO mutant Glycobiology (2005) 15(3): 259-269
    Howard, D. R., Fukuda, M., Fukuda, M. N., and Stanley, P. (1987) The GDP-fucose:N-acetylglucosaminide 3-alpha-L-fucosyltransferases of LEC11 and LEC12 Chinese hamster ovary mutants exhibit novel specificities for glycolipid substrates. J. Biol. Chem., 262, 16830-16837.
    Zhang, A., Potvin, B., Zaiman, A., Chen, W., Kumar, R., Phillips, L., and Stanley, P. (1999) The gain-of-function Chinese hamster ovary mutant LEC11B expresses one of two Chinese hamster FUT6 genes due to the loss of a negative regulatory factor. J. Biol. Chem., 274, 10439-10450.


EXAMPLES
Cell Lines
The recombinant CHO/DG44 cell line CHO-IgG was established earlier in our laboratory by stable transfection of the dihydrofolate reductase-deficient CHO cell line, CHO/DG44 (Urlaub et al., 1986, Proc Natl Acad Sci USA. 83 (2): 337-341) with an expression vector containing an antibody expression cassette comprising nucleotide sequences encoding light and heavy chain of a therapeutic monoclonal antibody (Trastuzumab (Herceptin®)). Generation of the cell line RMD-CHO-IgG started from the existing CHO-IgG cell line. Both cell lines were maintained in serum-free medium.
Gene Optimization and Synthesis
The amino acid sequence for the oxidoreductase Rmd (Pseudomonas aeruginosa PAO1; 304 amino acids) (GenBank Accession No. GenBank: AAG08839.1) was reverse translated and the resulting nucleotide sequence optimized by knockout of cryptic splice sites and RNA destabilizing sequence elements, optimisation for increased RNA stability and adaptation of codon usage to match the requirements of CHO cells (Cricetulus griseus).
Construction of the RMD Expression Plasmid
The synthesized RMD-construct was cut with EcoRI and Bgl II and dephoshorylated with calf intestinal phosphatase. The digested and dephosphorylated insert was ligated into a pre-digested bicistronic expression vector which allows coordinated co-expression of RMD and green fluorescent protein from a bicistronic message (gfp). The expression plasmid is equipped with a Neomycin resistance gene allowing for direct selection of cells that have stably integrated the bicistronic expression cassette. General procedures for constructing expression plasmids are described in Sambrook, J., E. F. Fritsch and T. Maniatis: Cloning I/II/III, A Laboratory Manual New York/Cold Spring Harbor Laboratory Press, 1989, Second Edition.
Conversion of Antibody-Producing CHO-IgG Cells into Cells Having a Blocked De Novo Pathway
CHO-IgG cells stably expressing the IgG1-type therapeutic antibody Trastuzumab were stably transfected with the RMD-gfp transgene by electroporation according to the manufacturer's instructions (MicroPorator, PEQLAB Biotech, Germany). 24 h after electroporation transfectants were selected in alpha-MEM containing the antibiotic G418. The G418-resistant clones were then isolated by limiting dilution cloning, i.e. they were resuspended in this selective medium and seeded into 96 well plates at dilutions where the likelihood of obtaining a colony from a single cell is greater 95% based on poisson statistics. To assure monoclonality, cells grown within the 96 wells were isolated and again seeded into 96 well plates at limiting dilution. After these two rounds of single cell cloning, a couple of the isolated single cell clones were expanded into larger volumes. Afterwards, they were adapted to growth in suspension. Using the described electroporation protocol a transformation efficiency of approximately 2000 per 2×106 electroporated cells was achieved as assessed from gfp-fluorescence distribution in the culture dishes (FIG. 2).
Clone Screening by Fluorescence Microscopy
Single cell clones were seeded into 96 well plates and screened for successful RMD-integration by monitoring of GFP-fluorescence with an Olympus IX-50 (Olympus Optical Co., Europe) fitted with a cmount adapter. For GFP-scan a fluorescence-filter at 200-fold extension was used versus phase contrast. Images were edited by Viewfinder lite application. Additionally, mRNA expression of the RMD transgene was confirmed by RT-PCR analysis. Successful expression of the RMD transgene was confirmed by RT-PCR using an RMD-specific set of primers (FIG. 3).
Fucose Feeding Experiment:
Determination of the Minimum Required Amount of Fucose Analogue in Culture Medium:
Currently, Fucose analogs are not routinely used in cell culture and are thus still expensive. In order to identify the most cost efficient fucose analogue concentration, we needed to determine the minimum required amount of fucose analogue that was sufficient to completely rescue the fucosylation status of heterologously expressed antibodies secreted from RMD-co-expressing cells. Antibody expressing CHO cells carrying the RMD transgene were cultured in medium containing varying concentrations of fucose and fed with a feed mix supplemented with that same amount of fucose. Cells were grown for 12 days before harvesting the cell culture supernatant. The supernatants were analysed by lectin blotting using biotinylated PSA lectin (pisum sativum) that specifically recognizes the alpha-1,6-linked core-fucose. Lectin blotting was conducted using the Vecstatin Elite ABC Kit (Vector Labs, USA) according to the manufacturers instructions. FIG. 4 demonstrates that an almost complete rescue of core-fucosylation was achieved when media and feeds were supplemented with 0.03 mM Fucose.
Production of Monoclonal Antibodies Comprising a Fucose Analogue on their N-Linked Glycomoieties
Antibody expressing CHO cells carrying the RMD transgene are cultured in medium containing 0.03 mM 1,2,3,4-tetraacetyl-6-azido-fucose (custom synthesized by Glykoteam GmbH Hamburg) and fed with a feed mix supplemented with 0.03 mM 1,2,3,4-tetraacetyl-6-azido-fucose. Cells are inoculated at 2×105 cells/ml in said growth medium. The shaker tubes are incubated at 180 rpm, 37° C., 7.5% pCO2. The culture is stopped after 7 days when the cells still showed a vitality>80% and cell culture supernatants are harvested. Viable cell density is measured with an automatic cell counter, Vi-CELLTM XR (Beckman Coulter, Fullerton, Calif.), using trypan blue exclusion.
Purification of Fucose Analogue Containing Monoclonal Antibodies by Protein A Affinity Chromatography
Fucose analogue containing antibodies secreted from these cells are purified by protein A affinity chromatography. Following sterile filtration by 0.2 μm filter, the supernatant is loaded onto a Protein-A-Sepharose mini column. 0.5 ml column support material with a total capacity of 10 mg are used. The column is equilibrated with 5 column volumes of 20 mM sodium phosphate, pH 7.0 at gravity flow. After protein binding at a slow flow rate, the column was washed twice with the equilibration buffer. Then the antibody is eluted with 4 column volumes 0.1 M glycine buffer, pH 3.0 at gravity flow. Fractions of 1 ml are collected and immediately neutralized with 1 M Tris-HCl, pH 9.
Labelling Azido-Fucose Containing Antibodies with Alkynyl-Biotin
The purified antibody containing 6-azido-fucose linked to its N-glycan core-position is subjected to a copper-mediated click chemistry coupling reaction with Biotin alkyne (Cat. No. B10185, Invitrogen). The click reaction is performed as described in the Click-iT® Protein Reaction Buffer Kit (Catalog no. C10276 (Invitrogen, Life Technologies Inc.) according to the manufacturers instructions. Briefly, the following components are added to a 1.5 mL microcentrifuge tube:

    
    
        200 μg in a maximum volume of 50 μL of azido-fucose-labeled antibody in 50 mM Tris-HCl, pH 8.0
        100 μL of the Click-iT® reaction buffer from the kit containing a final concentration of 40 μM alkynyl-Biotin.
        Sufficient volume of 18 megaOhm water for a final volume of 160 μL

The tube is then capped and vortexed for 5 seconds. 10 μL of CuSO4 (Component B) are added and the tube is again vortexed for 5 seconds. Then, 10 μL of Click-iT® reaction buffer additive 1 solution from the kit are added and the tube is again vortexed for 5 seconds. After 2-3 minutes, but not longer than 5 minutes, 20 μL of Click-iT® reaction buffer additive 2 solution are added and the tube is again vortexed for 5 seconds. The tube is then rotated end-over-end for 20 minutes using a rotator.

Analysis of Biotin-Labelled Antibodies

Part I Determination of Labelling Specificity:

    
    


600 μL of methanol are added to the reaction mixture and the mixture is briefly vortexed. 150 μL of chloroform are added and the mixture is vorteced briefly. 400 μL of 18 megaOhm water are then added and the mixture is vortexed briefly. The tube is then centrifuged for 5 minutes at 13,000×g, then carefully removed and as much of the upper aqueous phase as possible is discarded while leaving the interface layer containing the protein precipitate intact. Note: The upper phase is bright orange. The lower phase is colorless if biotin is used. 450 μL of methanol are then added to the tube and the tube is again vortexed briefly. The tube is then centrifuged for 5 minutes at 13,000×g to pellet the protein. The supernatant is discarded. Again 450 μL of methanol are added to the tube and the tube is vortexed briefly. The tube is again centrifuged and the supernatant is discarded. The pellet is allowed to air-dry for 15 minutes at ambient temperature and then resolubilized in non-reducing 1D gel electrophoresis sample loading buffer.
Samples are separated on 1D SDS-PAGE gels with and without reducing agent TCEP (Invitrogen) and blotted to a PVDF membrane (Immobilon-P (PVDF-Membrane 0.2 μm) [Millipore, Cat. IPVH00010]). The blotted PVDF membrane is blocked 30 min. at RT with 1× Carbo-Free Blocking solution ([VectorLabs Cat. No. SP5040], Vector Labs, USA) and then incubated with Streptavidin-HRP-conjugate (VECTASTATIN Elite ABC Kit; VectorLabs Cat. No. PK6100, Vector Labs, USA). The blotmembrane is then washed 3×5 min in PBS-T (1×PBS [pH 7.4]+0.05% Tween 20). TMB-substrate [Seramun, Cat. S-002-2-TMB prec] is dispersed across the blot membrane and the membrane is incubated for 0.5-5 min at ambient temperature. The reaction is stopped by washing with MilliQ H2O. The developed membrane is then air-dried and scanned. In the non-reduced sample lane a band at approximately 150 KDa apparent molecular mass is detected, representing the full length antibody. In the reducing sample lane, only the band migrating at an apparent molecular weight of 50 KDa, representing the heavy chain is detected as a biotinylated band whereas the light chain band migrating at  ̃25 KDa apparent molecular mass is only detected after secondary Coomassie staining. This result demonstates that the label has specifically attached to the heavy chain which is in line with the expectation that labelled fucose residues are exclusively found on the glycomoiety linked to ASN 297 (Kabat) of the heavy chain.
Part II: Assessment of Labelling Efficiency
In order to determine the efficiency of the Fucose-mediated labelling, we needed to determine the remaining amount of unlabelled N-glycans per antibody. The avidin-biotin complex is the strongest known noncovalent interaction (Ka=1015 M−1) between a protein and ligand. The bond formation between biotin and avidin is rapid and, once formed, is unaffected by extremes of pH, temperature, organic solvents and most denaturing agents. Monovalent streptavidin is an engineered recombinant form of streptavidin which is a tetramer but only one of the four binding sites is functional. [Horvath et al. 2006] This single binding site has 10-14 mol/L affinity and cannot cause cross-linking Bound monovalent streptavidin causes a biotinylated antibody to shift its apparent molecular mass in nondenaturing SDS-PAGE (Humbert et al. 2005) by 60 KDa per presented biotin, if monovalent steptavidin is available in excess during complex formation. 10 μg of click-reacted, biotinylated antibody sample is incubated with 10 μg (an excess amount) of monovalent Streptavidin (60 KDa) (xxx) and then analyzed on a NuPAGE 4-12% gel using the buffers of Kasarda et al. (2010). Bands representing molecular masses of 60, 150, 210 and 270 KDa indicate free streptavidin (60 KDa), completely unconjugated antibody (150 KDa), antibody with one biotinylated fucose residue (210 KDa), antibody with fully biotinylated fucose residue (270 KDa). Labelling efficiency is calculated from the ratio of fully biotinylated antibody and unbound or singly biotinylated antibody molecules.

## Claims

1. A eukaryotic cell for producing a molecule comprising a fucose analogue, wherein
(i) in said cell the GDP-L-fucose synthesis pathway originating from GDP-D-mannose is blocked due to the presence of at least one enzyme which uses GDP-6-deoxy-D-lyxo-4-hexulose as a substrate, wherein the enzyme does not catalyze the reaction which converts GDP-6-deoxy-D-lyxo-4-hexulose into GDP-L-fucose, and
(ii) said cell comprises a GDP-L-fucose analogue, wherein the GDP-L-fucose analogue is a substrate for a fucosyltransferase and enters the cell from extracellular medium.

2. The cell of claim 1, wherein the enzyme which uses GDP-6-deoxy-D-lyxo-4-hexulose as a substrate is selected from the group consisting of GDP-6-deoxy-D-lyxo-4-hexulose reductase (RMD), GDP-perosamine synthetase (Per), GDP-6-deoxy-D-talose synthetase (GTS), GDP-fucose synthetase Cys109Ser-(GFS-Cys109Ser) mutant, GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), preferably GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) in combination with GDP-L-colitose synthase (ColC), and variants thereof.

3. The cell of claim 1, wherein said cell
(i) does not comprise an enzymatically active GDP-mannose dehydratase (GMD) or comprises a GDP-mannose dehydratase (GMD) having a reduced enzymatic activity,
(ii) does not comprise an enzymatically active GDP-Fucose synthetase (GFS) or comprises a GDP-Fucose synthetase (GFS) having a reduced enzymatic activity, and/or
(iii) does not comprise an enzymatically active alpha-1,3-fucosyltransferase.

4. The cell of claim 1, wherein the cell is a vertebrate cell.

5. The cell of claim 4, wherein the vertebrate cell is a mammalian, a fish, an amphibian, a reptilian cell or an avian cell.

6. The cell of claim 5, wherein
(i) the mammalian cell is a human, hamster, canine or monkey cell,
(ii) the fish cell is a Ictalurus punctatus (channel catfish) cell,
(iii) the amphibian cell is a Xenopus laevis cell,
(iv) the reptilian cell is an Iguana iguana cell, or
(v) the avian cell is an avian retina cell, or an avian somite cell.

7. A method for producing a molecule which comprises a fucose analogue comprising the steps of:
(i) providing a eukaryotic cell according to claim 1, and
(ii) isolating the molecule comprising a fucose analogue from the cell in i).

8. The method of claim 7, further comprising the steps of:
(iii) covalently coupling a pharmaceutically active compound via the fucose analogue to the molecule comprising said fucose analogue, thereby obtaining a conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound.

9. A conjugate comprising a molecule which comprises a fucose analogue and a pharmaceutically active compound obtainable by the method of claim 8, wherein the pharmaceutically active compound is a cytotoxic drug or a pharmacokinetic half-life extender.

10. A conjugate which comprises a protein or polypeptide comprising one or more of the following structures: —NG-cF*—Yo-C,
wherein each is attached to an N-glycosylation site comprised in said protein or polypeptide,
NG is an N-linked glycomoiety of said protein or polypeptide,
cF* is a core fucose analogue,
Y is a spacer unit, wherein o is an integer of 0 or 1, and
C is a pharmaceutically active compound,
wherein the pharmaceutically active compound is a cytotoxic drug or a pharmacokinetic half-life extender.

11. The conjugate of claim 10, wherein the glycomoiety is an N-linked glycomoiety of the complex type.

12. The conjugate of claim 10, wherein the polypeptide is an antibody heavy chain (H).

13. A conjugate which comprises a protein or polypeptide comprising one or more EGF-like repeats comprising a serine and/or threonine residue to which the following structure: —F*-Yp-C
is attached, wherein
F* is a fucose analogue moiety directly linked to said serine and/or threonine residue,
Y is a spacer unit, wherein p is an integer of 0 or 1, and
C is a pharmaceutically active compound,
wherein the EGF-like repeats have independently from each other an amino acid sequence according to SEQ ID NO: 10 or are a variant thereof which is at least 90% identical to the amino acid sequence according to SEQ ID NO: 10.

14. The conjugate of claim 13, wherein the polypeptide is an antibody heavy chain (H).

15. A conjugate which comprises a polypeptide comprising one or more of the following structures: —NG-cF*—Yo—C,
wherein each is attached to an N-glycosylation site comprised in said polypeptide,
NG is an N-linked glycomoiety of said polypeptide,
cF* is a core fucose analogue,
Y is a spacer unit, wherein o is an integer of 0 or 1, and
C is a pharmaceutically active compound,
wherein the polypeptide is an antibody heavy chain (H).

16. An antibody comprising two conjugates as defined in claim 15.

17. The method of claim 1, wherein the GDP-L-fucose analogue comprises one or more reactive or activated substitutions selected from chemical groups listed in functional group A or functional group B of Table 2.

18. The method of claim 1, wherein the GDP-L-fucose analogue is a peracetylated fucose analogue.