GLYCAN-BASED ANTIBODY-DRUG CONJUGATES
Genetically engineered antibodies containing non-native N-glycosylated sites, preparation of the antibodies in yeast and fungi, site-specific conjugation of drugs to these antibodies, and methods of treatment utilizing these antibodies are described herein.
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This application is a divisional application of U.S. patent application Ser. No. 15/493,720, filed Apr. 21, 2017, which claims the benefit of U.S. Provisional Patent Application No. 62/325,497, filed Apr. 21, 2016, which is herein incorporated by referenced in its entirety.
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLYThe sequence listing of the present application is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file name “24059-US-DIV-SEQTXT-07APRIL2022.txt”, creation date of Apr. 7, 2022, and a size of 229 Kb. This sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTIONThe present invention relates to engineered immunoglobulin comprising mutations in the constant domains useful in antibody-drug conjugates (ADCs), methods of treatment utilizing the ADCs and methods of preparing the ADCs.
BACKGROUNDMonoclonal antibodies (mAbs) represent one of the fastest growing and most important sectors of the pharmaceutical market (Walsh, 2014). Antibodies (Abs) are unique molecules that provide the ability to target cell-associated and soluble antigens in a highly specific manner. This targeting can be used to block activities such as receptor-ligand interactions, influence or induce target-specific biological processes such as complement activities and immune cell-mediated cytotoxic activities, or modulate inflammation. However, efficient target cell killing, especially in the context of a solid tumor remains a limitation for many conventional mAbs (Schrama et al, 2006; Ricart, 2007). Increasing the versatility and effectiveness of these molecules will be a crucial focus as the next generation of antibody-based therapeutics is developed. One of the primary advancements in recent years is the resurgence of ADCs, particularly in the area of oncology (Flygare, 2013; Mullard, 2013). ADCs are comprised of a targeting vehicle and a linker that provides a stable support for the drug to prevent off-target release but allow effective release at the target location (Alley et al, 2010). Using the same strategy, Abs can also be conjugated to radioisotopes, peptides, or other macromolecules such as RNA (Ricart, 2011). However, to date, ADCs have been most often used for the delivery of drug payloads to improve cytotoxicity of a mAb to a known target (e.g. trastuzumab in the case of Her2; also known as Herceptin), which concomitantly increases the therapeutic index of an otherwise intolerable cytotoxic therapy (Burris, 2013).
While important technical challenges such as an optimal drug:antibody ratio (DAR) and methods of linker attachment (cleavable vs. non-cleavable) have been addressed to improve the characteristics of the current generation of ADCs, important limitations still exist (Panowski, 2013; Boylan, 2013). These hurdles include more efficient manufacture of ADCs, increased product homogeneity, and improving the sophistication of the chemistry available to allow broadening the scope of ADCs to include combining Abs with peptides and hormones.
It has been shown that site-specific targeting of a cytotoxic agent to an Ab not only improves the homogeneity of the drug product but also the therapeutic index and efficacy of the ADC (Junutula, 2008; Junutula, 2012). However, all current site-specific targeting technologies have significant limitations. Using engineered Cysteine (Cys) residues allows for a large degree of site specificity but does not prevent targeting to native Cys residues within the Ab protein, thus resulting in residual heterogeneity while likely decreasing the stability of the molecule through the disruption of native disulfide bonds, as well as complicating manufacture of an Ab that now contains free thiol residues (native Abs typically only contain paired Cys residues that are engaged in disulfide bonds). Recent technologies that rely on the incorporation of non-native amino acids are a step forward from engineered Cys residues because they allow for unique chemistry that is notpresent in the 20 amino acid code (Axup, 2012; Zimmerman, 2014). Incorporation of non-native amino acids also allows for more discrete control of the number of sites of conjugation. However scale-up and the subsequent manufacture of mAbs in mammalian cell lines, e.g., CHO cells, expressing non-native amino acids and efficient incorporation of these non-native amino acids introduces new challenges. Several other new technologies have emerged, but each with its own limitations, including introducing site specific tags in the mAb, which could promote immunogenicity, or modifying the N-297 glycan, which limits or abolishes immune effector function (Panowski, 2013). Also, in each case, scalability is either challenging or an unknown. Thus, an opportunity remains for a practical and scalable site-specific modification technology that would permit linking Abs to a range of different payloads.
SUMMARY OF THE INVENTIONThe present invention relates to engineered Abs or fragments thereof, and in particular IgG Abs possessing one to ten mutations within the heavy chain constant domains, e.g, CH1, hinge, CH2, CH3, and Fc. These mutations create non-native N-glycosylation sites in the heavy chain constant domain. In one embodiment, the engineered Abs of the invention are expressed in yeast or filamentous fungal host cells, for example Pichia pastoris host cells. When the engineered Abs are expressed in yeast and filamentous fungi host cells genetically engineered to produce human N-glycans, N-glycans are efficiently incorporated into the non-native N-glycosylation site(s) of the heavy chain constant domain. The engineered Abs expressed in genetically engineered yeast and filamentous fungal host cells possess a high degree ofN-glycan occupancy without disrupting the normal folding or function of the Ab, and allow conjugation of a suitable amount of payload/drug to the Ab to form an ADC. In particular, the engineered Abs of the invention comprise galactose-terminated N-glycans, which can be oxidized by an oxidizing reagent to produce aldehyde groups. The reactive aldehyde groups, in the presence of a derivatized drug containing a reactive amine form a bond (e.g., the reactive amine, alkoxyamine, reacts with aldehyde groups to form an oxime bond), thereby conjugating the drug to the Ab. In one embodiment, the engineered IgG Ab or fragment thereof comprises a human IgG1 constant domain.
In one embodiment, the present invention provides an engineered IgG Ab or fragment thereof comprising one to ten mutations (or pairs of mutations) in the heavy chain constant domain which generate one to ten non-native N-glycosylation sites, the mutations being selected from the group consisting of S134N, G161T, G161S, N203 T, N203 S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, according to EU numbering. In one embodiment, the engineered IgG Ab or fragment thereof comprises a human IgG1 constant domain.
In one embodiment, the engineered IgG Ab or fragment thereof comprises at least one or two amino acid mutations (or a pair of mutations) in the heavy chain constant domain selected from S134N, G161T and S134N/G161T. In one embodiment, the engineered IgG Ab or fragment thereof comprises a human IgG1 constant domain.
In another embodiment, the engineered IgG Ab or fragment thereof comprises at least two amino acid mutations in the heavy chain constant domain selected from G161T/S134T and G161S/S134T. In one embodiment, the engineered Ab comprises a human IgG1 constant domain.
In another embodiment, the N-glycosylated non-native site of the engineered IgG Ab or fragment thereof is conjugated to a drug selected from the group consisting of a polymer, cytotoxic agent, a radionuclide, fluorescent or chemiluminescent labels, steroid, steroid receptor agonist, signal transduction inhibitor, a peptide and scFv.
The present invention also relates to engineered IgG Abs or fragments thereof, and in particular Abs possessing one to two mutations in the heavy chain variable framework domain which generate one to two non-native N-glycosylation sites, the mutations being selected from the group consisting of Q105N and S113N, according to Kabat numbering.
In an embodiment, the engineered IgG Ab or fragment comprising one to two mutations in the heavy chain variable framework domain is conjugated to a drug and is selected from the group consisting of a polymer, cytotoxic agent, a radionuclide, fluorescent or chemiluminescent labels, steroid, signal transduction inhibitor, a peptide and scFv.
In another embodiment, a method of treating a disease or cancer in a patient suffering from the disease or cancer is provided, the method comprising administering to the patient a therapeutically effective amount of any of the aforementioned engineered IgG Abs or fragments thereof which are conjugated to a drug.
In another embodiment, a method of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to ten non-native N-glycosylation sites (or pairing of mutations) in the heavy chain constant domain is provided, the method comprising:
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- (a) transforming a yeast or filamentous fungus host cell genetically engineered to produce N-glycans comprising terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2 or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 with a nucleic acid encoding an IgG heavy chain constant domain or fragment thereof, wherein the IgG heavy chain constant domain comprises one to ten amino acid mutations, and wherein the one to ten amino acid mutations generate at least one N-glycosylation site in the IgG heavy chain constant domain;
- (b) culturing the transformed host cell under conditions that allow the expression of the IgG heavy chain constant domain comprising terminal galactose residues,
- (c) contacting the expressed IgG heavy chain constant domain with a reagent that oxidizes the terminal galactose residues; and
- (d) conjugating a drug to the oxidized moiety of the terminal galactose residues.
In one embodiment, the yeast host cell used in the method of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to ten non-native N-glycosylation sites in the heavy chain constant domain is selected from the group consisting of Pichia pastoris (Komagataella pastoris), Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia piperi, Pichia stiptis, Pichia methanolica, Pichia minuta (Ogataea minuta, Pichia lindneri), Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorpha, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Neurospora crassa and Yarrowia lipolytica. In another embodiment, the yeast host cell is Pichia pastoris.
In another embodiment, the IgG Ab or fragment thereof prepared by the aforementioned method comprises one to ten mutations (or pairs of mutations) in the heavy chain constant domain polypeptide selected from the group consisting of S134N, G161T, G161S, N203T, N203S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, according to EU numbering. In one embodiment, the IgG heavy chain is a human IgG1 constant domain.
In another embodiment, methods of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to two non-native N-glycosylation sites in the heavy chain variable framework domain are also provided.
In another embodiment, a method of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to ten non-native N-glycosylation sites in the heavy chain constant domain is provided, the method comprising:
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- (a) transforming a yeast or filamentous fungus host cell genetically engineered to produce N-glycans comprising terminal sialic acid residues of the structure NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2 with a nucleic acid encoding an IgG heavy chain contain domain, wherein the IgG heavy chain comprises one to ten amino acid mutations (or pairs of mutations), and wherein the one to ten amino acid mutation generates at least one non-native N-glycosylation site in the IgG heavy chain constant domain;
- (b) culturing the transformed host cell under conditions that allow the expression of the IgG heavy chain constant domain comprising terminal sialic acid residues,
- (c) contacting the expressed IgG heavy chain constant domain with neuraminidase to remove the terminal sialic acid residues to form N-glycosylated heavy chain constant domain comprising terminal galactose residues;
- (d) contacting the expressed glycosylated heavy chain constant domain comprising terminal galactose residues of step (c), with a reagent that oxidizes the terminal galactose residues; and
- (e) conjugating a drug to the oxidized moiety of the terminal galactose residues.
In one embodiment, the IgG heavy chain is a human IgG1 constant domain.
Patents, patent applications, publications, product descriptions, and protocols are cited throughout this application, the disclosures of which are incorporated herein by reference in their entireties for all purposes. All references cited herein are incorporated by reference to the same extent as if each individual publication, database entry (e.g. GenBank sequences or GeneID entries), patent application, or patent, was specifically and individually indicated to be incorporated by reference. Citation of the references herein is not intended as an admission that the reference is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents.
DefinitionsSo that the invention may be more readily understood, certain technical and scientific terms are specifically defined below. Unless specifically defined elsewhere in this document, all other technical and scientific terms used herein have the meaning commonly understood by one of ordinary skill in the art to which this invention belongs.
As used herein, including the appended claims, the singular forms of words such as “a,” “an,” and “the,” include their corresponding plural references unless the context clearly dictates otherwise.
By “position” as used herein is meant a location in the sequence of a protein. Positions may be numbered sequentially, or according to an established format, for example the EU index for antibody numbering or the Kabat numbering.
Amino acid positions in a heavy chain constant domain include amino acid positions in the CH1, hinge, CH2, CH3, Fc, and are numbered according to the EU index numbering system (also referred as the “EU index of Kabat” or the “EU index for antibody numbering” or “EU numbering). See Kabat et al., “Sequence of proteins of Immunological interest”, 5th edition, U.S. Dept Health and Human Services, U.S. Gov. Printing Office, 1991.
Amino acid positions in a variable domain (for example, in framework4 of the heavy chain) are numbered according to the Kabat numbering system (Kabat 1991).
Kabat numbering is based on the seminal work of Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Publication No. 91-3242, published as a three volume set by the National Institutes of Health, National Technical Information Service (hereinafter “Kabat”). Kabat provides multiple sequence alignments of immunoglobulin chains from numerous species antibody isotypes. The aligned sequences are numbered according to a single numbering system, the Kabat numbering system. The Kabat sequences have been updated since the 1991 publication and are available as an electronic sequence database (latest downloadable version 1997). Any immunoglobulin sequence can be numbered according to Kabat by performing an alignment with the Kabat reference sequence. Herein the heavy chain variable sequences are numbered according to the Kabat reference sequence.
The term “CH1” domain as used herein refers to the first constant domain of an IgG heavy chain that extends from about amino acid position 118-215 of the EU numbering system.
The term “hinge region” as used herein refers to the portion of a heavy chain that attaches the CH1 domain to the CH2 domain and comprises about 25 amino acid residues.
The term “CH2 domain” as used herein refers to the portion of a heavy chain IgG constant domain that extends from about amino acid positions 231-340 of the EU numbering system.
The term “CH3 domain” as used herein refers to the heavy chain IgG constant domain that extends from the N-terminus of the CH2 domain from about amino acid positions 341-445 of the EU numbering system.
The term “cytotoxic agent” as used herein refers to the effect of an agent that has a cytotoxic effect on a cell (i.e., an agent that can cause cell death).
The term “drug” as used herein refers to a compound including a compound, a pharmaceutically active compound, element, agent, pharmaceutically active peptide or protein, or molecular entity.
In general, the basic Ab structural unit comprises a tetramer. Each tetramer includes two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa). The amino-terminal portion of each chain includes a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The carboxy-terminal portion of the heavy chain may define a constant region primarily responsible for effector function.
As used herein “fragment” with respect to “antibody” or “IgG” or “monoclonal antibody” refers to those fragments produced by digestion with various proteases, those produced by chemical cleavage and/or chemical dissociation and those produced by recombination or recombinant DNA technology so long as the fragment remains capable of specific binding to a target molecule. Examples of fragments include, but are not limited to, Fc, Fab, Fab′, F(ab′)2, Fv, and scFv fragments.
In an embodiment, the Ab or fragment thereof comprises a heavy chain constant region, e.g. a human constant region, such as γ1, γ2, γ3, or γ4 human heavy chain constant region or a variant thereof. In another embodiment, the Ab or antigen binding fragment comprises a light chain constant region, e.g. a human light chain constant region, such as lambda or kappa human light chain region or variant thereof. By way of example, and not limitation the human heavy chain constant region can be γ1 and the human light chain constant region can be kappa.
A “Fab fragment” is comprised of one light chain and the CH1 and variable regions of one heavy chain. The heavy chain of a Fab molecule cannot form a disulfide bond with another heavy chain molecule. A “Fab fragment” can be the product of papain cleavage of an Ab.
A “Fab′ fragment” contains one light chain and a portion or fragment of one heavy chain that contains the VH domain and the CH1 domain and also the region between the CH1 and CH2 domains, such that an interchain disulfide bond can be formed between the two heavy chains of two Fab′ fragments to form a F(ab′)2 molecule.
A “F(ab′)2 fragment” contains two light chains and two heavy chains containing a portion of the constant region between the CH1 and CH2 domains, such that an interchain disulfide bond is formed between the two heavy chains. A F(ab′)2 fragment thus is composed of two Fab′ fragments that are held together by a disulfide bond between the two heavy chains. An “F(ab′)2 fragment” can be the product of pepsin cleavage of an Ab.
The term “Fe domain” as used herein refers to the portion of a heavy chain constant domain contains the hinge region (i.e., residue 216 in IgG, taking the first amino acid residue of the heavy chain constant domain to be 114), and CH2, and CH3 domains and ending at the C-terminus of the Ab.
The “Fv region” comprises the variable regions from both the heavy and light chains, but lacks the constant regions.
As used herein, a “chimeric Ab” is an Ab having the variable domain from a first Ab and the constant domain from a second Ab, where the first and second Abs are from different species. (U.S. Pat. No. 4,816,567; and Morrison et al., (1984) Proc. Natl. Acad. Sci. USA 81: 6851-6855). Typically the variable domains are obtained from an antibody from an experimental animal (the “parental Ab”), such as a rodent, and the constant domain sequences are obtained from human Ab, so that the resulting chimeric Ab will be less likely to elicit an adverse immune response in a human subject than the parental (e.g. rodent) antibody.
Typically, human light chains are classified as kappa and lambda light chains. Furthermore, human heavy chains are typically classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively. Within light and heavy chains, the variable and constant regions are joined by a “J” region of about 12 or more amino acids, with the heavy chain also including a “D” region of about 10 more amino acids. See generally, Fundamental Immunology Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y. (1989).
The variable regions of each light/heavy chain pair form the Ab binding site. Thus, in general, an intact Ab has two binding sites. Except in bifunctional or bispecific Abs, the two binding sites are, in general, the same.
Typically, the variable domains of both the heavy and light chains comprise three hypervariable regions, also called complementarity determining regions (CDRs), located within relatively conserved framework regions (FR). The CDRs are usually aligned by the framework regions, enabling binding to a specific epitope. In general, from N-terminal to C-terminal, both light and heavy chains variable domains comprise FR1, CDR1, FR2, CDR2, FR3, CDR3 andFR4. The assignment of amino acids to each domain is, generally, in accordance with the definitions of Sequences of Proteins of Immunological Interest, Kabat, et al.; National Institutes of Health, Bethesda, Md.; 5th ed.; NIH Publ. No. 91-3242 (1991); Kabat (1978) Adv. Prot. Chem. 32:1-75; Kabat, et al., (1977) J. Biol. Chem. 252:6609-6616; Chothia, et al., (1987) J Mol. Biol. 196:901-917 or Chothia, et al., (1989) Nature 342:878-883.
As used herein, the term “IgG” refers to IgG1, IgG2, IgG3 and IgG4. In an embodiment, IgG is IgG1. In one embodiment, the IgG1 is human IgG1.
As used herein, the term “hypervariable region” refers to the amino acid residues of an Ab that are responsible for antigen-binding. The hypervariable region comprises amino acid residues from a “complementarity determining region” or “CDR” (i.e. CDRL1, CDRL2 and CDRL3 in the light chain variable domain and CDRH1, CDRH2 and CDRH3 in the heavy chain variable domain). See Kabat et al. (1991); see also Chothia and Lesk (1987) J Mol. Biol. 196: 901-917 (defining the CDR regions of an Ab by structure).
As used herein, the term “framework” or “FR” residues refers to those variable domain residues other than the hypervariable region residues defined herein as CDR residues.
The phrase “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to use promoters, polyadenylation signals, and enhancers.
A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
As used herein, the expressions “cell,” “cell line,” and “cell culture” are used interchangeably and all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that not all progeny will have precisely identical DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
“Treat” or “treating” means to administer a therapeutic agent, such as a composition containing any of the genetically engineered Abs of the present invention, internally or externally to a subject or patient having one or more disease symptoms, or being suspected of having a disease, for which the agent has therapeutic activity. Typically, the agent is administered in an amount effective to alleviate one or more disease symptoms in the treated subject or population, whether by inducing the regression of or inhibiting the progression of such symptom(s) by any clinically measurable degree. The term further includes a postponement of development of the symptoms associated with a disorder and/or a reduction in the severity of the symptoms of such disorder. The terms further include ameliorating existing uncontrolled or unwanted symptoms, preventing additional symptoms, and ameliorating or preventing the underlying causes of such symptoms. Thus, the terms denote that a beneficial result has been conferred on a vertebrate subject with a disorder, disease or symptom, or with the potential to develop such a disorder, disease or symptom.
As used herein, the term “therapeutically effective amount” or “effective amount” refers to an amount of an engineered Ab drug conjugate or engineered Ab fragment thereof, that when administered alone or in combination with an additional therapeutic agent to a cell, tissue, or subject is effective to prevent or ameliorate the disease or condition to be treated. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions. When applied to an individual active ingredient administered alone, a therapeutically effective dose refers to that ingredient alone. When applied to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
As used herein, the terms “N-glycan” refers to an N-linked oligosaccharide, for example, one that is attached by an asparagine-N-acetylglucosamine linkage to an asparagine residue of a polypeptide. N-linked glycoproteins contain an N-acetylglucosamine residue linked to the amide nitrogen of an asparagine residue in the protein. The predominant sugars found on 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 post-translationally in the Golgi apparatus for N-linked glycoproteins.
Typically, 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). Usually, N-glycan structures are presented with the non-reducing end to the left and the reducing end to the right. The reducing end of the N-glycan is the end that is attached to the Asn residue comprising the glycosylation site on the protein. 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 Man.3GlcNAc2 (“Man3”) core structure which is also referred to as the “triammnose 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 has five or more mannose residues. A “complex” type N-glycan 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. ComplexN-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). ComplexN-glycans may also have intrachain substitutions comprising bisecting GlcNAc and core fucose (“Fuc”). Complex N-glycans may also have multiple antennae on the “trimannose core,” often referred to as “multiple antennary glycans.” A “hybrid” N-glycan 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 various N-glycans are also referred to as “glycoforms.”
With respect to complex N-glycans, the terms “G-2”, “G-1”, “G0”, “G1”, “G2”, “A1”, and “A2” mean the following. “G-2” refers to an N-glycan structure that can be characterized as Man3GlcNAc2; the term “G-1” refers to an N-glycan structure that can be characterized as GlcNAcMan3GlcNAc2; the term “G0” refers to an N-glycan structure that can be characterized as GlcNAc2Man3GlcNAc2; the term “G1” refers to an N-glycan structure that can be characterized as GalGlcNAc2Man3GlcNAc2; the term “G2” refers to an N-glycan structure that can be characterized as Gal2GlcNAc2Man3GlcNAc2; the term “A1” refers to an N-glycan structure that can be characterized as NANAGal2Gal2GlcNAc2Man3GlcNAc2; and, the term “A2” refers to an N-glycan structure that can be characterized as NANA2Gal2GlcNAc2Man3GlcNAc2. Unless otherwise indicated, the terms G-2”, “G-1”, “G0”, “G1”, “G2”, “A1”, and “A2” refer to N-glycan species that lack fucose attached to the GlcNAc residue at the reducing end of the N-glycan.
With respect to multiantennary N-glycans, the term “multiantennary N-glycan” refers to N-glycans that further comprise a GlcNAc residue on the mannose residue comprising the non-reducing end of the 1,6 arm or the 1,3 arm of the N-glycan or a GlcNAc residue on each of the mannose residues comprising the non-reducing end of the 1,6 arm and the 1,3 arm of the N-glycan. Thus, multiantennary N-glycans can be characterized by the formulas GlcNAc(2-4)Man3GlcNAc2, Gal(1-4)GlcNAc(2-4)Man3GlcNAc2, or NANA(1-4)Gal(1-4)GlcNAc(2-4)Man3GlcNAc2. The term “1-4” refers to 1, 2, 3, or 4 residues.
The term “GS3.5”, when used herein refers to the N-glycosylation structure GalGlcNAcMan5GlcNAc2.
The term “GS4.0”, when used herein refers to the N-glycosylation structure GlcNAc2Man3GlcNAc2.
The term “GS5.0”, when used herein refers to the N-glycosylation structure Gal2GlcNAc2Man3GlcNAc2.
The term “GS6.0”, when used herein refers to the N-glycosylation structure NANA2Gal2GlcNAc2Man3GlcNAc2.
The term “non-native N-glycosylation site” as used herein refers to any consensus (N-X-S/T, wherein X is any amino acid except proline) N-glycosylation site incorporated by mutation into an IgG that is not observed on naturally occurring IgG molecules (e.g. N-297). Moreover, while Asn-297 is the N-glycosylation site typically found in murine and human IgG molecules (Kabat et al, Sequences of Proteins of Immunological Interest, 1991), this site doesn't necessarily have to be maintained for function. Using known methods for mutagenesis, the skilled artisan can alter a DNA molecule encoding an Ig of the present invention so that the N-glycosylation site at Asn-297 is deleted.
As used herein, the term “predominantly” or variations such as “the predominant” or “which is predominant” will be understood to mean the glycan species or collective species that has the highest mole percent (%) of total N-glycans after the glycoprotein has been analyzed by mass spectrometry (e.g. Q-ToF) or enzymatically released N-glycans analyzed by mass spectroscopy (e.g. MALDI-TOF MS) or HPLC. For example, if a composition consists of species A in 40 mole percent, species B in 35 mole percent and species C in 25 mole percent, the composition comprises predominantly species A, and species B would be the next most predominant species. Furthermore, if a composition contains a mixture of species where 60% contain terminal galactose and 40% contain terminal sialic acid the composition will be defined has having predominantly terminal galactose.
As used herein, a glycoprotein composition “lacks” or “is lacking” a particular sugar residue, such as fucose or galactose, when no detectable amount of such sugar residue is present on the N-glycan structures at any time. For example, in preferred embodiments of the present invention, the glycoprotein compositions are produced by lower eukaryotic organisms, as defined above, including yeast and fungi [e.g., Pichia sp.; Saccharomyces sp.; Kluyveromyces sp.; Aspergillus sp.], and will “lack fucose,” because the cells of these organisms do not have the enzymes needed to produce fucosylated N-glycan structures. Thus, the term “essentially free of fucose” encompasses the term “lacking fucose.” However, a composition may be “essentially free of fucose” even if the composition at one time contained fucosylated N-glycan structures or contains limited, but detectable amounts of fucosylated N-glycan structures.
The term “mole percent” of a glycan present in a preparation of a N-glycosylated Ab refers to the molar percent of a particular glycan present in the pool of N-linked oligosaccharides released when the N-glycosylated Ab preparation is treated with PNGase and then quantified by a method that is not affected by glycoform composition, for instance, labeling a PNGase released glycan pool with a fluorescent tag such as 2-aminobenzamide and then separating by high performance liquid chromatography or capillary electrophoresis and then quantifying glycans by fluorescence intensity, or MALDI-TOF mass spectrometry. For example, 50 mole percent NANA2Gal2GlcNAc2Man3GlcNAc2 means that 50 percent of the released glycans are NANA2Gal2GlcNAc2Man3GlcNAc2 and the remaining 50 percent are comprised of other N-linked oligosaccharides. In embodiments, the mole percent of a particular glycan in a preparation of glycoprotein will be between 20% and 100%, preferably above 25%, 30%, 35%, 40% or 45%, more preferably above 50%, 55%, 60%, 65% or 70% and most preferably above 75%, 80% 85%, 90% or 95%.
OverviewThe present invention provides engineered Abs, in particular IgG Abs or fragments thereof comprising one to ten mutations (or pairs of mutations) in the heavy chain constant domain which generate one to ten non-native N-glycosylation sites. As shown in the Examples (see Example 1 and Example 14), the non-native N-glycosylation sites provide specific targeting sites for drug conjugates. In one embodiment, the engineered Abs, or fragments thereof of the invention are expressed in yeast and filamentous fungi host cells that have been engineered to produce human like N-glycans of the structure: Gal(1-4)GlcNAc(1-4)Man3GlcNAc2, Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 or NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2. In some embodiments, engineered Abs or fragments thereof expressed in these engineered yeast and filamentous fungi host cells comprise N-glycans where the predominant glycoform comprise the following structures: Gal(1-4)GlcNAc(1-4)Man3GlcNAc2 or Gal(1-2)GlcNAc(1-2)Man5GlcNAc2. In some embodiments, engineered Abs or fragments thereof expressed in glycoengineered yeast and filamentous fungi host cells comprise N-glycans in the non-native N-glycosylation sites comprising predominantly terminal sialylated residues (NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2), which in turn, can be converted into terminal galactose residues by an enzymatic reaction.
In some embodiments, the engineered Abs comprise N-glycans at the non-native N-glycosylation sites which do not disrupt the normal folding or function of the mAb, and allow the efficient, uniform conjugation of drugs such as toxins, peptides or bioactive sugar moieties. The DAR of the conjugated Ab can be modulated through the number of non-native N-glycosylation sites engineered into the Ab at specific sites as specified by the invention examples and the number of terminal galactose residues, which is driven by the N-glycan machinery of the recombinant host strain.
As background, the N-glycans are important molecules in biology that participate in a wide-range of different activities, from protein folding and trafficking to immune cell and host-pathogen interactions, owing in large part to the heterogeneity available from the modular, non-template nature of this protein modification, leading to an impressive breadth of potential forms that can be produced from a single core structure. N-glycans are also a key factor in biotherapeutic discovery and manufacture and limit the choice of expression system in many cases (Hossler, 2009; Schirrmann, 2008; Sethuraman, 2006). Examples of the differences in N-glycan pathways between humans and yeast can be found in
Directed and specific control of N-glycosylation can provide unique control over biology (e.g. modulation of inflammation, tissue and cell type targeting) but can also provide an opportunity for creating unique macromolecule chemistry, particularly in the case of the terminal sugars galactose and sialic acid (Ramya et al, 2013). Galactose oxidase (GO) is an enzyme that can specifically modify terminal galactose sugars present on an N-glycan, thus allowing for highly versatile and specific aldehyde-based chemistry that is not otherwise available in the 20 amino acid repetoire. However, the gly can heterogeneity that is confronted with conventional expression systems such as mammalian cells could complicate such an approach. For example, as demonstrated for human Erythropoietin (Nett et al, 2010; Restelli et al, 2006), proteins with exposed N-glycans can have huge variability in numbers of antennae (bi-, tri-, and tetra-) and amount of terminal sialic acid, whereas antibodies can contain differing amounts of fucose and galactose in addition to trace amounts of sialic acid (Li et al, 2006), all of which contributes to the considerable heterogeneity of mammalian N-glycans.
In one embodiment, the present invention provides an engineered IgG Ab or fragment thereof comprising one to ten mutations (or pairs of mutations) in the heavy chain constant domain, which generate one to ten non-native N-glycosylation sites, the mutations being selected from the group consisting of S134N, G161T, G161S, N203T, N203S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, according to EU numbering.
In one embodiment, the engineered IgG Ab or fragment thereof comprises at least one or two amino acid mutations in the heavy chain constant polypeptide selected from S134N, G161T and S134N/G161T.
In another embodiment, the engineered IgG Ab or fragment thereof comprises at least two amino acid mutations in the heavy chain constant domain selected from G161T/S134T and G161 S/S134T.
In one embodiment, the engineered heavy chain constant domains comprise, at the non-native N-glycosylated sites, predominantly complex N-glycans having the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2. In one embodiment, engineered heavy chain constant domains comprise, at the non-native N-glycosylation sites, predominantly complex N-gly cans having the structure Gal2GlcNAc2Man3GlcNAc2 (also referred to as GS5.0 N-glycans in
In another embodiment, the engineered heavy chain constant domains comprise, atthe non-native N-glycosylated sites, predominantly hybrid N-glycans having the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2.
In another embodiment, the engineered heavy chain constant domains comprise, at the non-native N-glycosylated sites, predominantly N-glycans having the structure NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2.
In another embodiment, the engineered IgG Abs or fragments thereof having non-native N-glycosylation sites comprise N-glycans wherein about 50 to about 100 mole % of the N-glycans comprise the structure: Gal2GlcNAc2Man3GlcNAc2Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 or NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2. In another embodiment, the engineered IgG Abs or fragments thereof having non-native N-glycosylation sites comprise N-glycans where about 80 to about 100 mole % of the N-glycans comprise the structure: Gal2GlcNAc2Man3GlcNAc2, Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 or NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2.
In one embodiment, the engineered Abs or fragments thereof are expressed in host cells capable of producing a composition of Abs or fragments thereof comprising N-glycans where the predominant glycoform comprise a Gal2GlcNAc2Man3GlcNAc2 N-glycan structure lacking fucose, wherein said structure is present at a level that is at least about 5 mole percent more than the next predominant N-glycan structure in the composition. In one embodiment, the engineered IgG Ab or fragments thereof comprise a predominant Gal2GlcNAc2Man3GlcNAc2N-glycan structure lacking fucose, wherein said structure is present at a level of at least about 10 mole percent to about 25 mole percent more than the next predominantN-glycan structure in the composition. In one embodiment, the engineered IgG Abs or fragments thereof comprise a predominant Gal2GlcNAc2Man3GlcNAc2 N-glycan structure lacking fucose, wherein said structure is present at a level that is at least about 25 mole percent to about 50 mole percent more than the next predominant N-glycan structure in the composition. In one embodiment, the engineered IgG Abs or fragments thereof comprise a predominant Gal2GlcNAc2Man3GlcNAc2 glycan structure lacking fucose, wherein said structure is present at a level that is greater than about 50 mole percent more than the next predominant glycan structure in the composition. In one embodiment, the engineered IgG Abs or fragments thereof comprise a predominant Gal2GlcNAc2Man3GlcNAc2 N-glycan structure lacking fucose, wherein said structure is present at a level that is greater than about 75 mole percent more than the next predominant glycan structure in the composition. In still another embodiment, the engineered IgG Abs or fragments thereof comprise a predominant Gal2GlcNAc2Man3GlcNAc2 N-glycan structure lacking fucose wherein said structure is present at a level that is greater than about 90 mole percent more than the next predominant glycan structure in the composition. MALDI-TOF analysis of N-glycans of an IgG having a predominant (greater than 95 mole %) Gal2GlcNAc2Man3GlcNAc2 lacking fucose is shown in
In another embodiment, the aforementioned IgG Ab or fragment thereof used for genetic engineering in its heavy chain constant domain is selected from the group consisting of anti-Her2, anti-Her2/neu (Herceptin), anti-glycoprotein IIb/IIIa (Abciximab), anti-TNF-α (Adalimumab, Certolizumab pegol, Golimumab, Infliximab), anti-CD52 (Alemtuzumab), anti-IL-2Rα (CD25) (Basiliximab), anti-BAFF (Belimumab), anti-Vascular endothelial growth factor (VEGF) (Bevacizumab), anti-CD30 (Brentuximab vedotin), anti-IL-1β (Canakinumab), anti-epidermal growth factor receptor (EGFR) (Cetuximab), anti-IL-2Rα receptor (CD25) (Daclizumab), anti-RANK Ligand (Denosumab), anti-Complement C5 (Eculizumab), anti-CD11a (Efalizumab), anti-CD33 (Gemtuzumab), anti-CD20 (Ibritumomab tiuxetan), anti-CTLA-4 (Ipilimumab (MDX-101)), anti-T cell CD3 Receptor (Muromonab-CD3), anti-alpha-4 (α4) integrin, anti-(Natalizumab), anti-CD20 (Ofatumumab), anti-Immunoglobulin E (IgE) (Omalizumab), anti-RSV F protein (Palivizumab), anti-epidermal growth factor receptor (Panitumumab), anti-VEGF-A (Ranibizumab), anti-CD20 (Rituximab), anti-Anti-IL-6R (Tocilizumab, Atlizumab), anti-CD20 (Tositumomab), anti-ErbB2 (Trastuzumab), anti-IL-12/IL-23 (Ustekinumab), anti-integrin α4β7 (Vedolizumab), anti-CD274, anti-β-amyloid, anti-4-1BB, anti-5AC, anti-5T4, anti-ACVR2B, anti-adenocarcinomaantigen, anti-AGS-22M6, anti-alpha-fetoprotein, anti-angiopoietin 2, anti-angiopoietin 3, anti-anthrax toxin, anti-AOC3 (VAP-1), anti-, anti-B7-H3, anti-Bacillus anthracis, anti-BAFF, anti-beta amyloid, anti-B-lymphoma cell, anti-C242 antigen, anti-C5, anti-CA-125, anti-carbonic anhydrase 9 (CA-IX), anti-cardiac myosin, anti-CCL11 (eotaxin-1), anti-CCR4, anti-CCR5, anti-CD11/CD18, anti-CD125, anti-CD140a, anti-CD147 (basigin), anti-CD15, anti-CD152, anti-CD154 (CD40L), anti-CD19, anti-CD2, anti-CD20, anti-CD200, anti-CD22, anti-CD221, anti-CD23, anti-CD25, anti-CD27, anti-CD28, anti-CD28, anti-CD3, anti-CD3 epsilon, anti-CD30 (TNFRSF8), anti-CD33, anti-CD37, anti-CD38, anti-CD4, anti-CD40, anti-CD41, anti-CD44, anti-CD5, anti-CD51, anti-CD52, anti-CD56, anti-CD6, anti-CD70, anti-CD74, anti-CD79B, anti-CD80, anti-CEA, anti-CFD, anti-ch4D5, anti-CLDN18.2, anti-C. difficile, anti-clumping factor A, anti-CSF2, anti-CTLA-4, anti-cytomegalovirus, anti-CMV gp B, anti-DLL4, anti-DR5, anti-E. coli shiga toxin type-1 or 2, anti-EGFL7, anti-EGFR, anti-endotoxin, anti-EpCAM, anti-EpCAM/CD3, anti-episialin, anti-ERBB3, anti-Escherichia coli, anti-F protein RSV, anti-FAP, anti-fibrin II, beta chain, anti-fibronectin extra domain-B, anti-folate receptor 1, anti-Frizzled receptor, anti-ganglioside GD2, anti-GD2, anti-GD3 ganglioside, anti-GD3 ganglioside, anti-GMCSF receptor α-chain, anti-GPNMB, anti-Influenza, anti-Influenza hemagglutinin, anti-hepatitis B, anti-hepatitis B, anti-surface antigen, HER1, anti-HER2/neu, anti-HER2, CD3, anti-HER3, anti-HGF, anti-HGF, anti-HHGFR, anti-HIV-1, anti-HLA-DR, anti-HNGF, anti-Hsp90, anti-human scatter factor receptor kinase, anti-human TNF, anti-human beta-amyloid, anti-ICAM-1 (CD54), anti-IFN-α, anti-IFN-γ, anti-IgE, anti-IgE Fc region, anti-IGF-1 receptor, anti-IGF-I, anti-IgG4, anti-IGHE, anti-IL20, anti-IL-1beta, anti-IL-12/IL-23, anti-IL-13, anti-IL-17, anti-IL-17A, anti-IL-1β, anti-IL-22, anti-IL-23, anti-IL-4, anti-IL-5, anti-IL-6, anti-IL-6 receptor, anti-IL9, anti-ILGF2, anti-insulin-like growth factor I receptor (IGF-1R), anti-integrin α4β7, anti-integrin α4, anti-integrin α4β7, anti-integrin α5β1, anti-integrin α7β7, anti-integrin αIIbβ3, anti-integrin αvβ, anti-interferon receptor, anti-interferon α/β receptor, anti-interferon gamma-induced protein, anti-ITGA2, anti-ITGB2 (CD18), anti-KIR2D, anti-Lewis-Y antigen, anti-LFA-1 (CD11a), anti-lipoteichoic acid, anti-LOXL2, anti-L-selectin (CD62L), anti-LTA, anti-MCP-1, anti-mesothelin, anti-MS4A1, anti-MUC1, anti-mucin CanAg, anti-myostatin, anti-NARP-1, anti-NCA-90, anti-NGF, anti-N-glycolylneuraminic acid (NGNA), anti-NOGO-A, anti-Notch receptor, anti-NRP1, anti-Oryctolagus cuniculus, anti-OX-40, anti-oxLDL, anti-PCSK9, anti-PD-1, anti-PDCD1, anti-PDCD1, anti-PDGF-R α, anti-phosphate-sodium co-transporter, anti-phosphatidylserine, anti-prostatic carcinoma cells, anti-Pseudomonas aeruginosa, anti-rabies virus, anti-rabies virus glycoprotein, anti-RANKL, anti-respiratory syncytial virus, anti-RHD, anti-Rhesus factor, anti-RON, anti-RTN4, anti-sclerostin, anti-SDC1, anti-selectin P, anti-SLAMF7, anti-SOST, anti-sphingosine-1-phosphate, anti-TAG-72, anti-T-cell receptor, anti-TEM1, anti-tenascin C, anti-TFPI, anti-TGF beta 1, anti-TGF beta 2, anti-TGF-0, anti-TNF-α, anti-TRAIL-R1, anti-TRAIL-R2, anti-tumor antigen CTAA16.88, anti-MUC1 (tumor-specific glycan), anti-TWEAK receptor, anti-TYRP1 (glycoprotein 75), anti-VEGF-A, anti-VEGFR-1, anti-VEGFR2, anti-vimentin, anti-VWF, anti-IL-1, anti-IL-2, anti-IL-4, anti-IL-5, anti-IL-6, anti-IL-8, anti-IL-9, anti-IL-10, anti-IL-12, anti-IL-15, anti-IL-17, anti-IL-18, anti-IL-20, anti-IL-21, anti-IL-22, anti-IL-23, anti-IL-23R, anti-IL-25, anti-IL-27, anti-IL-33, anti-CD2, anti-CD4, anti-CD 11A, anti-CD14, anti-CD18, anti-CD19, anti-CD23, anti-CD25, anti-CD40, anti-CD40L, anti-CD20, anti-CD52, anti-CD64, anti-CD80, anti-CD147, anti-CD200, anti-CD200R, anti-TSLP, anti-TSLPR, anti-PD-1, anti-PDL1, anti-CTLA4, anti-VLA-4, anti-VEGF, anti-PCSK9, anti-α4β7-integrin, anti-E-selectin, anti-Fact II, anti-ICAM-3, anti-beta2-integrin, anti-IFNγ, anti-C5, anti-CBL, anti-LCAT, anti-CR3, anti-MDL-1, anti-GITR, anti-CGRP, anti-TRKA, anti-IGF1R, anti-GTC.
In one embodiment, the engineered IgG Ab or fragment thereof is human anti-Her2 Ab or a fragment thereof. In another embodiment, the engineered IgG Ab is human anti-PD-1 Ab or a fragment thereof.
In another embodiment, the engineered IgG Ab or fragment thereof is an anti-Her2 Ab comprising a heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 4-29, 31, 32, 33, 34, 35, 36, 37, 38, 39 and 40.
In another embodiment, the engineered IgG Ab or fragment thereof is an anti-mouse-PD-1 Ab comprising a heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 41-45.
In another embodiment, the engineered IgG Ab or fragment thereof is an anti-CS1 Ab comprising a heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 46-50.
In another embodiment, the engineered IgG Ab or fragment thereof is an anti-CD70 Ab comprising a heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 51-55.
In another embodiment, the present invention provides an engineered IgG Ab or fragment thereof comprising one to two mutations in the heavy chain framework domain which generate one to two non-native N-glycosylation sites, the mutations being selected from the group consisting of Q105N and S113N, according to Kabat numbering.
In one embodiment, the engineered heavy chain constant domain comprises, at the non-native N-glycosylated sites, predominantly complex N-glycans having the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2. In one embodiment, engineered heavy chain constant domain comprise, at the non-native N-glycosylation sites, predominantly complex N-gly cans having the structure Gal2GlcNAc2Man3GlcNAc2 (also referred to as GS5.0 N-glycans in
In another embodiment, the engineered heavy chain constant domain comprises, at the non-native N-glycosylated sites, predominantly hybrid N-glycans having the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2.
In another embodiment, the engineered heavy chain constant domain comprises, at the non-native N-glycosylated sites, predominantly N-glycans having the structure NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2
In another embodiment, the engineered IgG Ab having non-native N-glycosylation sites comprises N-glycans wherein about 50 to about 100 mole % of the N-gly cans comprise the structure: Gal2GlcNAc2Man3GlcNAc2, Gal(1-2)GlcNAc1-2Man5GlcNAc2 or NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2. In another embodiment, the engineered Ab having non-native N-glycosylation sites comprises N-glycans where about 80 to about 100 mole % of the N-glycans comprise the structure: Gal2GlcNAc2Man3GlcNAc2, Gal(1-2)GlcNAc1-2Man5GlcNAc2 or NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2.
In one embodiment, the aforementioned IgG Ab or fragment thereof used for genetic engineering in its heavy chain framework domain is selected from the Abs as described above.
Ab-Drug ConjugatesIn another embodiment, the engineered IgG Ab or fragment thereof is conjugated to a drug via the Ab's non-native N-glycosylated site. The drug is selected from the group consisting of a polymer, cytotoxic agent, a radionuclide, fluorescent or chemiluminescent labels, steroid, steroid receptor agonist, signal transduction inhibitor, a peptide and scFv.
In one embodiment, the drug is a polymer which increases the half-life of the engineered Ab or fragment thereof in the body of a subject. Suitable polymers include, but are not limited to, hydrophilic polymers which include but are not limited to polyethylene glycol (PEG) (e.g., PEG with a molecular weight of 2 kDa, 5 kDa, 10 kDa, 12 kDa, 20 kDa, 30 kDa or 40 kDa), dextran and monomethoxypolyethylene glycol (mPEG). Methods for pegylating proteins are known in the art and can be applied to the Abs of the invention. See, e.g., EP 0 154 316 and EP 0 401 384. Lee, et al., (1999) (Bioconj. Chem. 10:973-981) discloses PEG conjugated single-chain Abs. Wen, et al., (2001) (Bioconj. Chem. 12:545-553) disclose conjugating antibodies with PEG which is attached to a radiometal chelator (diethylenetriaminpentaacetic acid (DTPA)). For example, to pegylate an Ab, the Ab, or fragment thereof, typically is reacted with a reactive form of polyethylene glycol (PEG), such as a reactive ester or aldehyde derivative of PEG, under conditions in which one or more PEG groups become attached to the antibody or antibody fragment. In particular embodiments, the pegylation is carried out via an acylation reaction or an alkylation reaction with a reactive PEG molecule (or an analogous reactive water-soluble polymer). As used herein, the term “polyethylene glycol” is intended to encompass any of the forms of PEG that have been used to derivatize other proteins, such as mono (C1-C10) alkoxy- or aryloxy-polyethylene glycol or polyethylene glycol-maleimide.
The engineered IgG Ab or fragments thereof may also be conjugated to a cytotoxic agent such as diptheria toxin, Pseudomonas aeruginosa exotoxin A chain, ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins and compounds (e.g., fatty acids), dianthin proteins, Phytoiacca americana proteins PAPI, PAPII, and PAP-S, Momordica charantia inhibitor, curcin, crotin, Saponaria officinalis inhibitor, mitogellin, restrictocin, phenomycin, and enomycin.
The engineered IgG Ab and fragments thereof may also be conjugated with labels such as 99Tc, 90Y, 111In, 32P, 14C, 125I, 3H, 131I, 11C, 15O, 13N, 18F, 35S, 51Cr, 57To, 226Ra, 60Co, 59Fe, 57Se, 152Eu, 67CU, 217Ci, 211At, 212Pb, 47Sc, 109Pd, 234Th, and 40K, 157Gd, 55Mn, 52Tr, and 56Fe.
The engineered IgG Ab or fragment thereof may also be conjugated with fluorescent or chemilluminescent labels, including fluorophores such as rare earth chelates, fluorescein and its derivatives, rhodamine and its derivatives, isothiocyanate, phycoerythrin, phycocyanin, allophycocyanin, o-phthaladehyde, fluorescamine, 152Eu, dansyl, umbelliferone, luciferin, luminal label, isoluminal label, an aromatic acridinium ester label, an imidazole label, an acridimium salt label, an oxalate ester label, an aequorin label, 2,3-dihydrophthalazinediones, biotin/avidin, spin labels and stable free radicals.
The engineered IgG Ab or fragment thereof may also be conjugated to a steroid such as glucocorticoid.
The engineered IgG Ab or fragment thereof may also be conjugated to a steroid receptor agonist such as a glucocorticoid receptor agonist (e.g., mapracorat).
The engineered IgGAb or fragment thereof may also be conjugated to a signal transduction inhibitor such as dasatinib (see Wang et al., 2015).
The engineered IgG Ab or fragment thereof may also be conjugated to a peptide, e.g., activated GLP-1 receptor agonistic peptide (see Example 9)
The engineered IgG Ab or fragment thereof may also be conjugated to a scFv.
Any method known in the art for conjugating the Ab molecules to the various moieties may be employed (see e.g., Axup, 2012; Tian, 2014; Jackson, 2014, WO2005047334, WO2005047336, WO200547337 and WO2006107124 (the disclosures of which are incorporated herein by reference) disclose chemically conjugating peptides or drug molecules to Fc fragment. Methods for conjugating Abs are conventional and very well known in the art.
ADC delivery of a drug moiety to its intracellular target occurs via a multistep sequence of events: binding to the cell surface, endocytosis, trafficking (within an endosome) to a lysosome, proteolytic degradation of the conjugate, and diffusion of the released drug moiety across the lysosomal or endosomal membrane toward its intracellular target and its interaction with the target. Therefore, the linker should be sufficiently stable while in circulation to allow delivery of the intact ADC to the target cell but, on the other hand, sufficiently labile to allow release of the drug moiety from the ADC once inside the targeted cell.
In an embodiment as described below in the method of preparing an engineered Ab-drug conjugate, the linker is comprised of an oxime linkage. In this regard, the terminal galactose residues of the human complex N-glycan or human hybrid N-glycan are specifically oxidized to produce chemically-reactive aldehyde groups utilizing an enzyme known as galactose oxidase (GO) as described e.g., in Cooper et al., 1959. The chemically reactive aldehyde group is receptive to direct conjugation with an alkoxyamine substrate forming a stable oxime bond as described e.g, in Ramya et al. 2013, and as described below and in Example 5.
Uses of Ab-Drug Conjugates ImmunoimagingIn another embodiment, the engineered IgG Ab-drug conjugates of the present invention can be used for in vivo immunoimaging. For this purpose, the Ab or fragment thereof is labeled by means which permit external visualization of its position or location within a subject or part thereof, such as an organ. Typically, an immunoimaging agent will be an Ab labeled directly (as with Technetium) or indirectly (as with chelated Indium) with a suitable radioisotope. After injection into the patient, the location of the conjugate may be tracked by a detector sensitive to particles emitted by the radiolabel, e.g., a gamma-scintillation camera in the case of a gamma emitter.
ImmunotherapyIn another embodiment, the engineered IgG Ab-drug conjugate of the present invention can be used to treat cancer or a disease, such as an autoimmune disease or an infectious disease, in a patient, such as a human or an animal (e.g., a dog or a cat) suffering from the cancer or the disease. Accordingly, methods of treating a disease or cancer in a patient suffering from the cancer or disease are provided, the methods comprising administering to the patient a therapeutically effective amount of the engineered IgG Ab or fragment thereof, which is conjugated to a drug.
With respect to cancer, the engineered Ab-drug conjugates can be used for inhibiting the multiplication of a tumor cell or cancer cell, causing apoptosis in a tumor or cancer cell, or for treating cancer in a patient by delivering a drug to a tumor cell or cancer cell.
The specificity of the Ab for a particular tumor cell or cancer cell can be important for determining those tumors or cancers that are most effectively treated. For example, the anti-HER2 mAb trastuzumab is known to be useful in treating HER+ tumors such as breast cancer and brain cancer.
Examples of cancers that can be treated with the engineered Ab-drug conjugates include, but are not limited to, solid tumors, including but not limited to: fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon cancer, colorectal cancer, kidney cancer, pancreatic cancer, bone cancer, breast cancer, ovarian cancer, prostate cancer, esophogeal cancer, stomach cancer, oral cancer, nasal cancer, throat cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, uterine cancer, testicular cancer, small cell lung carcinoma, bladder carcinoma, lung cancer, epithelial carcinoma, glioma, glioblastoma multiforme, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, skin cancer, melanoma, neuroblastoma, retinoblastoma, blood-borne cancers (including but not limited to: acute lymphoblastic leukemia “ALL”, acute lymphoblastic B-cell leukemia, acute lymphoblastic T-cell leukemia, acute myeloblastic leukemia “AML”, acute promyelocytic leukemia “APL”, acute monoblastic leukemia, acute erythroleukemic leukemia, acute megakaryoblastic leukemia, acute myelomonocytic leukemia, acute nonlymphocyctic leukemia, acute undifferentiated leukemia, chronic myelocytic leukemia “CML”, chronic lymphocytic leukemia “CLL”, hairy cell leukemia, multiple myeloma), acute and chronic leukemias (e.g., lymphoblastic, myelogenous, lymphocytic, and myelocytic leukemias), and Lymphomas (e.g., Hodgkin's disease, non-Hodgkin's Lymphoma, Multiple myeloma, Waldenstrom's macroglobulinemia, Heavy chain disease, and Polycythemia vera).
In another embodiment, the engineered Ab-drug conjugate can be administered concurrently with another anti-cancer agent such as a chemotherapeutic agent or with radiation therapy. In another embodiment, the chemotherapeutic agent or radiation therapy is administered prior or subsequent to administration of the engineered Ab-drug conjugate. Any one or a combination of the chemotherapeutic agents listed below can be administered. With respect to radiation, any radiation therapy protocol can be used depending upon the type of cancer to be treated. For example, but not by way of limitation, x-ray radiation can be administered; in particular, high-energy megavoltage (radiation of greater that 1 MeV energy) can be used for deep tumors, and electron beam and orthovoltage x-ray radiation can be used for skin cancers. Gamma-ray emitting radioisotopes, such as radioactive isotopes of radium, cobalt and other elements, can also be administered.
Examples of chemotherapeutic agents include, but are not limited to, methotrexate, taxol, L-asparaginase, mercaptopurine, thioguanine, hydroxyurea, cytarabine, cyclophosphamide, ifosfamide, nitrosoureas, cisplatin, carboplatin, mitomycin, dacarbazine, procarbizine, topotecan, nitrogen mustards, cytoxan, etoposide, 5-fluorouracil, BCNU, irinotecan, camptothecins, bleomycin, doxorubicin, idarubicin, daunorubicin, dactinomycin, plicamycin, mitoxantrone, asparaginase, vinblastine, vincristine, vinorelbine, paclitaxel, and docetaxel. drugs such as an alkylating agents such as a nitrogen mustard (e.g., cyclophosphamide, ifosfamide, trofosfamide, chlorambucil, melphalan), nitrosoureas (e.g., carmustine (BCNU), lomustine (CCNU)), alkylsulphonates (e.g., busulfan, treosulfan), triazenes (e.g., decarbazine), Platinum containing compounds (e.g., cisplatin, carboplatin); plant alkaloids, such as vinca alkaloids (e.g, vincristine, vinblastine, vindesine, vinorelbine), taxoids (e.g., paclitaxel, docetaxol); DNA topoisomerase inhibitors such as epipodophyllins (e.g., etoposide, teniposide, topotecan, 9-aminocamptothecin, camptothecin, crisnatol, mitomycins (e.g., mitomycin C); anti-metabolites such as anti-folates such as DHFR inhibitors (e.g., methotrexate, trimetrexate), IMP dehydrogenase inhibitors (mycophenolic acid, tiazofurin, ribavirin, EICAR) and ribonucleotide reductase inhibitors (e.g., hydroxyurea, deferoxamine), pyrimidine analogs such as uracil analogs (5-fluorouracil, floxuridine, doxifluridine, ratitrexed), cytosine analogs (e.g., cytarabine (ara C), cytosine arabinoside, fludarabine), and purine analogs (e.g., mercaptopurine, thioguanine); hormonal therapies, such as receptor antagonists, such as anti-estrogens (e.g., tamoxifen, raloxifene, megestrol), LHRH agonists (e.g., goscrclin, leuprolide acetate), and anti-androgens (e.g., flutamide, bicalutamide; retinoids/deltoids such as vitamin D3 analogs (e.g., EB 1089, CB 1093, KH 1060), photodynamic therapies (e.g., vertoporfin (BPD-MA), phthalocyanine, photosensitizer Pc4, demethoxy-hypocrellin A (2BA-2-DMHA)), cytokines (e.g., interferon-.alpha., interferon-.gamma., tumor necrosis factor), as well as other drugs, such as gemcitabine, velcade, revamid, thalamid, isoprenylation inhibitors (e.g., lovastatin), dopaminergic neurotoxins (e.g., 1-methyl-4-phenylpyridinium ion), cell cycle inhibitors (e.g., staurosporine), actinomycins (e.g., actinomycin D, dactinomycin), bleomycins, bleomycin A2, bleomycin B2, peplomycin), anthracyclines (daunorubicin, Doxorubicin (adriamycin), idarubicin, epirubicin, pirarubicin, zorubicin, mtoxantrone), MDRinhibitors (e.g., verapamil), and Ca.sup.2+ATPase inhibitors (e.g, thapsigargin)
The engineered Ab-drug conjugates can also be used for killing or inhibiting the replication of a cell that produces an autoimmune disease or for treating an autoimmune disease. Accordingly, the engineered Ab-drug conjugates can be used accordingly in a variety of settings for treating an autoimmune disease in a patient suffering from the autoimmune disease. For example, the conjugates can be used to deliver a drug to a target cell. Without being bound by theory, in one embodiment, the engineered Ab-drug conjugates associate with an antigen on the surface of a target cell, and the conjugate is then taken up inside a target-cell through receptor-mediated endocytosis. Once inside the cell, one or more specific peptide sequences (e.g., within a linker) are enzymatically or hydrolytically cleaved, resulting in release of a drug. The released drug is then free to migrate in the cytosol and induce cytotoxic or cytostatic activities. In another embodiment, the drug is cleaved from the engineered Ab-conjugate outside the target cell, and the drug subsequently penetrates the cell.
In another embodiment, the engineered Ab-drug conjugates bind to an autoimmune antigen which is on the surface of a cell. For example, the engineered Ab can bind to activated lymphocytes that are associated with the autoimmune disease state. In a further embodiment, the engineered Ab-drug conjugates kill or inhibit the multiplication of cells that produce an autoimmune antibody associated with a particular autoimmune disease.
Examples of autoimmune diseases that can be treated with the engineered Ab-drug conjugates include, but are not limited to, Th2 lymphocyte related disorders (e.g., atopic dermatitis, atopic asthma, rhinoconjunctivitis, allergic rhinitis, Omenn's syndrome, systemic sclerosis, and graft versus host disease); Th1 lymphocyte related disorders (e.g., rheumatoid arthritis, multiple sclerosis, psoriasis, Sjorgren's syndrome, Hashimoto's thyroiditis, Grave's disease, primary biliary cirrhosis, Wegener's granulomatosis and tuberculosis); and activated B lymphocyte related disorders (e.g., systemic lupus erythematosus, Goodpasture's syndrome, rheumatoid arthritis and type I diabetes). Other autoimmune diseasesinclude, butare notlimited to, active chronic hepatitis, Addison's disease, allergic alveolitis, allergic reaction, allergic rhinitis, Alport's Syndrome, anaphlaxis, ankylosing spondylitis, anti-phosholipid syndrome, arthritis, ascariasis, aspergillosis, atopic allergy, atropic dermatitis, atropic rhinitis, Behcet's disease, Bird-Fancier's Lung, bronchial asthma, Caplan's syndrome, cardiomyopathy, Celiac disease, Chagas' disease, chronic glomerulonephritis, Cogan's Syndrome, cold agglutinin disease, congenital rubella infection, CREST syndrome, Crohn's disease, cryoglobulinemia, Cushing's syndrome, dermatomyositis, discoid lupus, Dressler's syndrome, Eaton-Lambert syndrome, echovirus infection, encephalomyelitis, endocrine opthalmopathy, Epstein-Barr virus infection, equine heaves, erythematosis, Evan's syndrome, Felty's syndrome, fibromyalgia, Fuch's cyclitis, gastric atrophy, gastrointestinal allergy, giant cell arteritis, glomerulonephritis, goodpasture's syndrome, graft v. host disease, Graves' disease, Guillain-Barre disease, Hashimoto's thyroiditis, hemolytic anemia, Henoch-Schonlein Purpura, idiopathic adrenal atrophy, idiopathic pulmonary fibritis, IgA nephropathy, inflammatory bowel disease, insulin-dependent diabetes mellitus, juvenile arthritis, juvenile diabetes mellitus (Type I), Lambert-Eaton syndrome, laminitis, lichen planus, lupoid hepatitis, lupus, lymphopenia, Meniere's disease, mixed connective tissue disease, multiple sclerosis, myasthenia gravis, pernicious anemia, polyglandular syndromes, presenile dementia, primary agammaglobulinemia, primary biliary cirrhosis, psoriasis, psoriatic arthritis, Raynauds phenomenon, recurrent abortion, Reiter's syndrome, rheumatic fever, rheumatoid arthritis, Sampter's syndrome, schistosomiasis, Schmidt's syndrome, scleroderma, Shulman's syndrome, Sjorgen's syndrome, stiff-man syndrome, sympathetic ophthalmia, systemic lupus erythematosis, Takayasu's arteritis, temporal arteritis, thyroiditis, thrombocytopenia, thyrotoxicosis, toxic epidermalnecrolysis, TypeBinsulinresistance, Type Idiabetesmellitus, ulcerative colitis, uveitis, vitiligo, Waldenstrom's macroglobulemia, and Wegener's granulomatosis.
In another embodiment, methods for treating an autoimmune disease arealso provided that comprise administering to a patient in need thereof an effective amount of an engineered IgG Ab-drug conjugate alone or in combination another therapeutic agent known for the treatment of an autoimmune disease. Examples of anti-autoimmune disease agent include, but are not limited to, the following: cyclosporine, cyclosporine A, mycophenylate mofetil, sirolimus, tacrolimus, etanercept, prednisone, azathioprine, methotrexate, cyclophosphamide, aminocaproic acid, chloroquine, hydroxychloroquine, hydrocortisone, dexamethasone, chlorambucil, DHEA, danazol, bromocriptine, meloxicam and infliximab.
In another embodiment, methods for treating an infectious disease are provided which comprise administering to the patient suffering from the infectious disease a therapeutically effective amount of an engineered IgG Ab or fragment thereof conjugated to a drug. The engineered Ab-drug conjugates can be used accordingly in a variety of settings for the treatment of an infectious disease in a patient. The ADCs can be used to deliver a drug to a target cell. In one embodiment, the Ab binds to the infectious disease cell. In another embodiment, the engineered Ab-drug conjugate kills or inhibit the multiplication of cells that produce a particular infectious disease. Examples of infectious diseases that can be treated with the engineered Ab-drug conjugates include, but are not limited to, the following: bacterial diseases, such as diphtheria, pertussis, occult bacteremia, urinary tract infection, gastroenteritis, cellulites, epiglottitis, tracheitis, adenoid hypertrophy, retropharyngeal abcess, impetigo, ecthyma, pneumonia, endocarditis, septic arthritis, pneumococcal, peritonitis, bactermia, meningitis, acute purulent meningitis, urethritis, cervicitis, proctitis, pharyngitis, salpingitis, epididymitis, gonorrhea, syphilis, listeriosis, anthrax, nocardiosis, salmonella, typhoid fever, dysentery, conjunctivitis, sinusitis, brucellosis, tularemia, cholera, bubonic plague, tetanus, necrotizing enteritis, and actinomycosis; mixed anaerobic infections, such as syphilis, relapsing fever, leptospirosis, Lyme disease, rat bite fever, tuberculosis, lymphadenitis, leprosy, chlamydia, chlamydial pneumonia, trachoma, and inclusion conjunctivitis; systemic fungal diseases such as histoplamosis, coccidiodomycosis, blastomycosis, sporotrichosis, cryptococcsis, systemic candidiasis, aspergillosis, mucormycosis, mycetoma, and chromomycosis; rickettsial diseases such as typhus, Rocky Mountain Spotted Fever, ehrlichiosis, Eastern Tick-Borne Rickettsioses, rickettsialpox, Q fever and bartonellosis; parasitic diseases such as malaria, babesiosis, African sleeping sickness, Chagas' disease, leishmaniasis, Dum-Dum fever, toxoplasmosis, meningoencephalitis, keratitis, entamebiasis, giardiasis, cryptosporidiosis, isosporiasis, cyclosporiasis, microsporidiosis, ascariasis, whipworm infection, hookworm infection, threadworm infection, ocular larva migrans, trichinosis, Guinea worm disease, lymphatic Filariasis, loiasis, River Blindness, canine heartworm infection, schistosomiasis, swimmer's itch, Oriental lung fluke, Oriental liver fluke, fascioliasis, fasciolopsiasis, opisthorchiasis, tapeworm infections, hydatid disease, and alveolar hydatid disease; viral diseases such as measles, subacute sclerosing panencephalitis, common cold, mumps, rubella, roseola, Fifth Disease, chickenpox, respiratory syncytial virus infection, croup, bronchiolitis, infectious mononucleosis, poliomyelitis, herpangina, hand-foot-and-mouth disease, Bornholm disease, genital herpes, genital warts, aseptic meningitis, myocarditis, pericarditis, gastroenteritis, acquired immunodeficiency syndrome (AIDS), human immunodeficiency vims (HIV), Reye's syndrome, Kawasaki syndrome, influenza, bronchitis, viral “Walking” pneumonia, acute febrile respiratory disease, acute pharyngoconjunctival fever, epidemic keratoconjunctivitis, Herpes Simplex Virus 1 (HSV-1), Herpes Simplex Virus 2 (HSV-2), shingles, cytomegalic inclusion disease, rabies, progressive multifocal leukoencephalopathy, kuru, fatal familial insomnia, Creutzfeldt-Jakob disease, Gerstmann-Straussler-Scheinker disease, tropical spastic paraparesis, western equine encephalitis, California encephalitis, St. Louis encephalitis, Yellow Fever, Dengue, lymphocytic choriomeningitis, Lassa fever, hemorrhagic fever, Hantvims pulmonary syndrome, Marburg virus infections, Ebola virus infections and smallpox.
In yet another embodiment, methods for treating an infectious disease are provided which comprise administering to a patient suffering from the infectious disease an engineered IgG Ab-drug conjugate alone or in combination with another therapeutic agent that is an anti-infectious disease agent. Examples of anti-infectious disease agents include, but not limited to, beta.-lactam antibiotics, such as penicillin G, penicillin V, cloxacillin, dicloxacillin, methicillin, nafcillin, oxacillin, ampicillin, amoxicillin, bacampicillin, azlocillin, carbenicillin, mezlocillin, piperacillin and ticarcillin; aminoglycosides such as amikacin, gentamicin, kanamycin, neomycin, netilmicin, streptomycin and tobramycin; macrolides such as azithromycin, clarithromycin, erythromycin, lincomycin and clindamycin; tetracyclines such as demeclocycline, doxycycline, minocycline, oxytetracycline and tetracycline; quinolones such as cinoxacin, and nalidixic acid; fluoroquinolones such as ciprofloxacin, enoxacin, grepafloxacin, levofloxacin, lomefloxacin, norfloxacin, ofloxacin, sparfloxacin and trovafloxicin; polypeptides such as bacitracin, colistin and polymyxin B; sulfonamides such as sulfisoxazole, sulfamethoxazole, sulfadiazine, sulfamethizole and sulfacetamide; and other antibacterial agents, such as trimethoprim, sulfamethazole, chloramphenicol, vancomycin, metronidazole, quinupristin, dalfopristin, rifampin, spectinomycin and nitrofurantoin; and antiviral agents, such as general antiviral agents such as idoxuradine, vidarabine, trifluridine, acyclovir, famcicyclovir, pencicyclovir, valacyclovir, gancicyclovir, foscarnet, ribavirin, amantadine, rimantadine, cidofovir; antisense oligonucleotides, immunoglobulins and interferons; drugs for HIV infection such as tenofovir, emtricitabine, zidovudine, didanosine, zalcitabine, stavudine, lamivudine, nevirapine, delavirdine, saquinavir, ritonavir, indinavir, and drugs for treatment of metabolic disease such as nelfinavir.
Pharmaceutical Compositions Containing the Ab-Drug ConjugatesIn another embodiment, pharmaceutical compositions are provided comprising an effective amount of the engineered IgG Ab-drug conjugate and a pharmaceutical acceptable carrier. The pharmaceutical compositions can be in various forms for administration to a patient. For example, the composition can be in the form of a solid, liquid or gas (aerosol). Typical routes of administration include, without limitation, oral, topical, parenteral, sublingual, rectal, vaginal, ocular, intra-tumor, and intranasal. Parenteral administration includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques. In one embodiment, the compositions are administered parenterally. In another embodiment, the conjugate or compositions are administered intravenously. Such compositions are suitable for veterinary or human administration.
Pharmaceutical compositions can be formulated so as to allow a conjugate to be bioavailable upon administration of the composition to a patient. Compositions can take the form of one or more dosage units, where for example, a tablet can be a single dosage unit, and a container of a conjugate in injectable form can hold a plurality of dosage units.
Materials used in preparing the pharmaceutical compositions can be non-toxic in the amounts used. As evident to those of ordinary skill in the art that the optimal dosage of the active ingredient(s) in the pharmaceutical composition will depend on a variety of factors. Relevant factors include, without limitation, the type of patient, e.g., human or animal, the particular form of the engineered-Ab conjugate, the manner of administration, and the composition employed.
The pharmaceutically acceptable carrier or vehicle can be particulate, so that the compositions are, for example, in tablet or powder form. The carrier(s) can be liquid, with the compositions being, for example, an oral syrup or injectable liquid. In addition, the carrier(s) can be gaseous or particulate, so as to provide an aerosol composition useful in, e.g., inhalatory administration.
When intended for oral administration, the composition is preferably in solid or liquid form, where semi-solid, semi-liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.
As a solid composition for oral administration, the composition can be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like. Such a solid composition typically contains one or more inert diluents. In addition, one or more of the following can be present: binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, or gelatin; excipients such as starch, lactose or dextrins; disintegrating agents such as alginic acid, sodium alginate, Primogel, corn starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin, a flavoring agent such as peppermint, methyl salicylate or orange flavoring, and a coloring agent. When the composition is in the form of a capsule, e.g., a gelatin capsule, it can contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol, cyclodextrin or a fatty oil.
The composition can be in the form of a liquid, e.g., an elixir, syrup, solution, emulsion or suspension. The liquid can be useful for oral administration or for delivery by injection. When intended for oral administration, a composition can comprise one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer. In a composition for administration by injection, one or more of a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent can also be included.
The liquid compositions, whether they are solutions, suspensions or other like form, can also include one or more of the following: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or digylcerides which can serve as the solvent or suspending medium, polyethylene glycols, glycerin, cyclodextrin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. A parenteral composition can be enclosed in ampoule, a disposable syringe or a multiple-dose vial made of glass, plastic or other material. Physiological saline is an exemplary adjuvant. An injectable composition is preferably sterile.
Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
The effective amount of the engineered Ab-drug conjugate for treatment of a particular cancer or disease will depend on the nature of the cancer or disease and can be determined by standard clinical techniques. The dosage ranges for the administration of the disclosed engineered Ab-drug conjugates are those large enough to produce the desired effect in which the symptoms of the condition or disorder are ameliorated. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. In addition, in vitro or in vivo assays can optionally be employed to help identify optimal dosage ranges.
The precise dose to be employed in the pharmaceutical compositions will also depend on the age, condition, sex and extent of the disease in the patient, route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances.
Typically, the effective amount of the engineered Ab-drug conjugate is at least about 0.01% of a conjugate by weight of the composition. When intended for oral administration, this amount can be varied to range from about 0.1% to about 80% by weight of the pharmaceutical composition. In one embodiment, oral pharmaceutical compositions can comprise from about 4% to about 50% of the conjugate by weight of the composition. In yet another embodiment, present compositions are prepared so that a parenteral dosage unit contains from about 0.011% to about 2% by weight of the conjugate.
For intravenous administration, the composition can comprise from about 0.01 to about 100 mg of a conjugate per kg of the animal's body weight. In one embodiment, the composition can include from about 1 to about 100 mg of a conjugate per kg of the animal's body weight. In another embodiment, the amount administered will be in the range from about 0.1 to about 25 mg/kg of body weight of the conjugate.
Generally, the dosage of an Ab-conjugate administered to a patient is typically about 0.01 mg/kg to about 2000 mg/kg of the animal's body weight. In one embodiment, the dosage administered to a patient is between about 0.01 mg/kg to about 10 mg/kg of the animal's body weight. In another embodiment, the dosage administered to a patient is between about 0.1 mg/kg and about 250 mg/kg of the animal's body weight. In yet another embodiment, the dosage administered to a patient is between about 0.1 mg/kg and about 20 mg/kg of the animal's body weight. In yet another embodiment the dosage administered is between about 0.1 mg/kg to about 10 mg/kg of the animal's body weight. In yet another embodiment, the dosage administered is between about 1 mg/kg to about 10 mg/kg of the animal's body weight.
The Ab-conjugates can be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.). Administration can be systemic or local. Various delivery systems are known, e.g., encapsulation in liposomes, microparticles, microcapsules, capsules, etc., and can be used to administer a conjugate or composition. In certain embodiments, more than one conjugate or composition is administered to a patient.
The term “carrier” as used herein refers to a diluent, adjuvant or excipient, with which a conjugate is administered. Such pharmaceutical carriers can be liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. The carriers can be saline, gum acacia, gelatin, starch paste, talc, keratin, colloidal silica, urea, and the like. In addition, auxiliary, stabilizing, thickening lubricating and coloring agents can be used. In one embodiment, when administered to a patient, the Ab-conjugate or compositions and pharmaceutically acceptable carriers are sterile. Water is an exemplary carrier when the conjugate are administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical carriers also include excipients such as starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The compositions, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
The compositions can take the form of solutions, suspensions, emulsion, tablets, pills, pellets, capsules, capsules containing liquids, powders, sustained-release formulations, suppositories, emulsions, aerosols, sprays, suspensions, or any other form suitable for use. Other examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.
Typically, the carriers or vehicles for intravenous administration are sterile isotonic aqueous buffer solutions. Pharmaceutical compositions may also include a solubilizing agent or a local anesthetic such as lignocaine to ease pain at the site of the injection.
Pharmaceutical compositions for oral delivery can be in the form of tablets, lozenges, aqueous or oily suspensions, granules, powders, emulsions, capsules, syrups, or elixirs, for example. Orally administered compositions can contain one or more optionally agents, for example, sweetening agents such as fructose, aspartame or saccharin; flavoring agents; coloring agents; and preserving agents, to provide a pharmaceutically palatable preparation. Moreover, where in tablet or pill form, the pharmaceutical compositions can be coated to delay disintegration and absorption in the gastrointestinal tract thereby providing a sustained action over an extended period of time.
Pharmaceutical compositions can also be administered topically, in which case the carrier may be in the form of a solution, emulsion, ointment or gel base. For transdermal administration, the pharmaceutical composition can be in the form of a transdermal patch or an iontophoresis device. Topical formulations can comprise a concentration of an engineered Ab-drug conjugate of from about 0.05% to about 50% w/v (weight per unit volume of composition), in another embodiment, from 0.1% to 10% ow/v.
Methods of Preparing Engineered mAb-Drug Conjugates
In another embodiment, a method of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to ten non-native N-glycosylation sites in the heavy chain constant domain is provided, the method comprising:
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- (a) transforming a yeast or filamentous fungus host cell genetically engineered to produce N-glycans comprising terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2) or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2, with a nucleic acid encoding an IgG heavy chain contain domain, wherein the IgG heavy chain constant domain comprises one to ten amino acid mutations, and wherein the amino acid mutations generate at least one non-native N-glycosylation site in the IgG heavy chain constant domain;
- (b) culturing the transformed host cell under conditions that allow the expression of IgG heavy chain constant domain comprising terminal galactose residues;
- (c) contacting the expressed IgG heavy chain constant domain with a reagent that oxidizes the terminal galactose residues; and
- (d) conjugating a drug to the oxidized moiety of the terminal galactose residues.
The yeast host cell used in step (a) of the method of preparing a conjugated N-glycosylated IgG Ab or fragment thereof containing one to ten non-native N-glycosylation sites in the heavy chain constant domain is selected from the group consisting of Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia minuta (Ogataea minuta, Pichia lindneri), Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorphs, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Neurospora crassa and Yarrowia lipolitica. In an embodiment, the yeast host cell is Pichia pastoris.
Methods for producing yeast host cells and filamentous fungal host cells genetically engineered to produce human-like complex N-glycans containing terminal galactose residues (Gal(1-4)GlcNAc(1-4)Man3GlcNAc2), or human-like hybrid N-gly cans containing galactose residues (Gal(1-2)GlcNAc(1-2)Man5GlcNAc2) are described in the art, e.g., in U.S. Pat. No. 8,815,544; Bobrowicz P, et al., Glycobiology 14: 757-766; Li et al., (2006) Nat. Biotechnol. 24: 210-215; Zha, 2013. In one embodiment, the yeast host cell is a Pichia pastoris host cell that has been engineered to produce N-glycans comprising predominantly the Gal(1-4)GlcNAc(1-4)Man3GlcNAc2 glycoforms. In another embodiment, the yeast host cell is a Pichia pastoris host cell that has been engineered to produce N-glycans comprising predominantly the Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 glycoforms. In another embodiment, the yeast host cell is a Pichia pastoris host cell that has been engineered to produce N-glycans comprising predominantly the Gal2GlcNAc2Man3GlcNAc2 glycoforms.
The nucleic acid encoding a heavy chain constant domain, in useful embodiments may comprise the complete heavy chain of the IgG Ab e.g., anti-Her2 IgG1 (SEQ ID NO: 1), wherein the heavy chain constant domain can be modified to effect the substitution of the relevant amino acid residues by site directed mutagenesis as in Example 1. Alternatively, the nucleic acid encoding the heavy chain domain may be prepared by chemical synthesis, wherein oligonucleotides are designed based on the specific amino acid sequence of the antibody mutant.
In an embodiment, the aforementioned nucleic acid comprises a nucleotide sequence encoding an anti-Her2 heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 4-29, 31, 32, 33, 34, 35, 36, 37, 38, 39 and 40.
In another embodiment, the aforementioned nucleic acid comprises a nucleotide sequence encoding an anti-mouse PD-1 heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 41-45.
In another embodiment, the aforementioned nucleic acid comprises a nucleotide sequence encoding an anti-CS1 heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 46-50.
In another embodiment, the aforementioned nucleic acid comprises a nucleotide sequence encoding an anti-CD70 heavy chain mutant polypeptide comprising an amino acid sequence selected from SEQ ID NOs: 51-55.
In another embodiment, the yeast or filamentous host cell is transformed with the complete nucleotide sequences encoding one or both of the heavy and light chain sequences of an IgG Ab, e.g., anti-Her2 IgG1 heavy and light chain sequences (SEQ ID NOs: 1 and 2, respectively) or a fragment thereof. Transformation is effected by inserting the nucleotide sequences encoding the heavy and/or light chains of the antibody into a recombinant vector and operably linked to control sequences required for expression of the heavy and light chain in the transformed host cell. One of skill in the art may make a selection among vectors and expression control sequences well known in the art. In an embodiment, the vector is an expression vector in which the nucleotide sequence encoding the heavy and light chain of the antibodies is operably linked to additional segments required for transcription of the nucleotide sequence. The vector is typically derived from plasmid (see Example 1) or viral DNA. A number of suitable expression vectors for expression in the host cells mentioned herein are commercially available or described in the literature.
In another embodiment of the foregoing method, the IgG Ab or fragment thereof prepared by the aforementioned method comprises one to ten mutations (or pairs of mutations) in the heavy chain constant polypeptide selected from the group consisting of S134N, G161T, G161S, N203T, N203S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, according to EU numbering.
Following transformation of the yeast or filamentous host cells (step a), the transformed host cells are cultured (step b) in a nutrient medium suitable for production of the engineered Ab or fragment thereof using methods known in the art. For example, the host cells may be cultured by shake flask, small-scale or large-scale fermentation (including continuous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermenters performed in a suitable medium and under conditions allowing the heavy and light chains to be expressed and isolated. Suitable media are available from commercial suppliers or may be prepared according to published composition. The produced Abs or fragments thereof contain an engineered N-glycosylated heavy chain constant domain comprising an N-glycan comprising terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2) or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2.
In an embodiment, the engineered Ab prepared by the foregoing method comprises about 50 to about 100 mole % of N-glycan with terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2) or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2. In another embodiment, the engineered antibody prepared by the foregoing method comprises about 80 to about 100 mole % of N-gly can with terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2) or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2.
The aforementioned expressed Ab comprising the N-glycosylated heavy chain constant domain may be recovered from the nutrient medium by methods known in the art, e.g., centrifugation, filtration, extraction, evaporation, or precipitation.
The engineered Ab may then be purified by a variety of procedures known in the art including, but not limited to, chromatography (e.g. ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g. preparative isoelectric focusing), differential solubility (e.g. ammonium sulfate precipitation), SDS-PAGE, or extraction. In an embodiment, the engineered Ab is purified by protein A chromatography (See Example 3.
The purified engineered Ab containing the expressed N-glycosylated heavy chain constant domain is then contacted with a reagent that oxidizes the terminal galactose residues of the N-glycan to generate an aldehyde (step c).
In an embodiment, the reagent is the enzyme galactose oxidase (GAL, D-galactose: oxygen 6-oxidoreductase; EC 1.1.3.9, commercially available from Sigma purified from Dactylium dendroites; also referred herein as GO) which specifically oxidizes terminal galactose residues at the C-6 position to generate an aldehyde group (see e.g., Cooper et al., 1959). The aldehyde group is a chemically reactive group that can be directly conjugated with a reactive amine group such as an alkoxyamine (also known as aminooxy) present in a derivatized-drug to form a stable oxime bond (Ramya et al., 2013) between the derivatized drug and the engineered N-glycan.
The term “derivatived drug” refers to a drug that contains or is modified to contain a reactive amine.
The term “reactive amine” refers to any nitrogen-containing functional group that can be covalently attached or bonded through a nitrogen atom to an aldehyde functional group by a simple chemical condensation reaction. Examples of other reactive amines include but are not limited to hydrazine, hydrazide, phenylhydrazine, phenylhydrazide, phenoxyamine, semicarbazide and thiosemicarbazide.
With respect to carrying out oxidation of the terminal galactose residues of the engineered N-glycosylated Abs, the Ab is present in aqueous solution at a concentration of about 0.1 to 100 mg/ml, 0.5 to 50 mg/ml, 1.0 to 20 mg/ml, or 0.5 to 20 mg/ml (see e.g., Copper et al., and Rayma et al., 2013). The enzyme GO generally is used at a pH about 5.5 to about 8.0. The influence of pH, substrate concentration, buffers and buffer concentrations on enzyme reaction are reported in Cooper et al., supra.
In another embodiment utilizing GO as the oxidizing reagent, the purified engineered Abs containing the expressed N-glycosylated heavy chain constant domain can be contacted with GO by producing the GO in vivo in the yeast and filamentous fungi host cells that have been genetically engineered to produce N-glycosylated mAbs containing N-glycans comprising terminal galactose residues. For example, a yeast or host cell can also be transformed with a plasmid containing the nucleotide sequence encoding GO (e.g., GO from Fusarium graminearum, SEQ ID NO: 57; see Paukner, 2014; Anasontzis, 2014; Deacon, 2004). In another embodiment, the terminal galactose residue of the engineered N-gly can of the Ab can alsobe oxidized to form aldehyde groups utilizing chemical oxidizing reagents. Examples of chemical oxidizing reagents include, but are not limited to periodic acid, paraperiodic acid, sodium metaperiodate and potassium metaperiodate. Among these, oxygen acids and salts thereof are preferred since secondary or undesirable side reactions are less frequent. For a general discussion, see Jackson, 1944, in Organic Reactions 2, p. 341; Bunton, 1965, Oxidation in Organic Chemistry, Vol. 1 Wiberg, ed., Academic Press, New York, p. 367.
Oxidation of the engineered Abs with these chemical oxidizing reagents can be carried out by known methods. In the oxidation, the engineered Ab is generally present in the form of an aqueous solution at a concentration generally of less than 100 mg/ml, or 1 to 20 mg/ml. When an oxygen acid or salt thereof is used as the oxidizing agent, it is used generally in the form of an aqueous solution, and the concentration is generally 0.001 to 10 mM and preferably 1.0 to 10 mM. The amount of the oxygen acid or salt thereof depends on the kind of antibody, but generally it is used in excess, for example, ten to 100 times as much as the amount of the oxidizable N-glycan. The optimal amount, however, can be determined by routine experimentation.
Following oxidation of the engineered N-glycosylated Ab, the Ab can be conjugated to a drug by reacting the Ab with a drug having a reactive amine group selected from the group consisting of hydrazine, hydrazide, phenylhydrazine, phenylhydazide, alkoxyamine, phenoxyamino, semicarbazide and thiosemicarbazide groups.
In a useful embodiment, the reactive amine group is an alkoxyamine (aminooxy) group. Drugs modified to contain a reactive amino group such as alkoxyamine can be synthesized by methods known in the art (Jayasekara, 2014; Trimaille 2014; Su 2005; Singh 2005) and are also commercially available (e.g., the amino oxy activated C5-linker containing DMI (chemically synthesized by Concortis Biosystems in San Diego, Calif., see Example 10; aminooxy activated Exendin-4-peptide chemically synthesized by Biopeptekin Malvern, Pa., see Example 9; and aminooxy activated CF633 dye chemically synthesized by Biotium in Hayward, Calif., Example 5).
In an embodiment, a solution of the oxidized engineered Ab at a concentration from about 0.5 to 20 mg/ml is mixed with an amine derivative of a drug (molar ratios of reactive amine group to antibody aldehyde ranging from about 1 to about 10,000) and the solution incubated for from about 1 to 72 hours, preferably in the dark. Suitable temperatures are from 0° to 37° C. and pH may be from about 6 to 8.
The aforementioned method of preparing Ab-drug conjugate can also be used to prepare Ab-drug conjugate, wherein the engineered Ab contains one to two non-native N-glycosylation sites in the heavy chain framework domain as is described above.
In another embodiment, a method of preparing a conjugated N-glycosylated Ab or fragment thereof containing one to ten non-native N-glycosylation sites in the heavy chain constant domain is provided, the method comprising:
-
- (a) transforming a yeast or filamentous fungus host cell genetically engineered to produce N-glycans comprising terminal sialic acid residues (NANA(1-4)Gal(1-4)GlcNAc(1-4)Man3GlcNAc2) with a nucleic acid encoding a heavy chain contain domain, wherein the heavy chain comprises one to ten amino acid mutations, and wherein the one to ten amino acid mutation generates at least one non-native N-glycosylation site in the heavy chain constant domain;
- (b) culturing the transformed yeast host cell under conditions that allow the expression of the heavy chain constant domain comprising terminal sialic acid residues,
- (c) contacting the expressed heavy chain constant domain with neuraminidase to remove the terminal sialic acid residues to form N-glycosylated heavy chain constant domain comprising terminal galactose residues;
- (d) contacting the expressed glycosylated heavy chain constant domain comprising terminal galactose residues of step (c), with a reagent that oxidizes the terminal galactose residues;
- (e) conjugating a drug to the oxidized moiety of the terminal galactose residues.
Methods for producing yeast host cells and filamentous fungal host cells genetically engineered to produce human-like complex N-glycans containing terminal sialic acid residues are described e.g. in U.S. Pat. Nos. 8,715,963; 7,863,020; Nett et al., (2011), Yeast 28(3):237-52 (2011); Hamilton et al., Curr Opin Biotechnol. 18(5):387-92 (2007); Hamilton et al., (2006) Science 313: 1441-1443.
Methods of transforming the yeast strains to produce N-glycans with terminal sialic acid residues, preparing mutated nucleic acids containing the non-native N-glycosylation sites, and culturing steps (steps a-b) are as described above (strains containing N-gly cans with terminal galactose residues). With respect to step (c), N-glycans comprising sialic acid residues can be desialyated using the enzyme Acetyl-neuroaminyl hydrolase (neuraminidase, New England Biolabs, Ipswich, Mass.) according to the manufacturer's recommended reaction conditions, to efficiently remove the sialic acid residues leaving predominantly terminal galactose residues. Step (d) of contacting the expressed glycosylated heavy chain constant domain with a reagent, e.g., GO or a chemical reagent, that oxidizes the terminal galactose residues, and step (e) of conjugating a drug to the oxidized moiety of the terminal galactose residues is as described above.
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The anti-HER2 (trastuzumab) IgG1 H chain and L chain sequences (Seq ID NO: 1 and 2, respectively) were incorporated into a single ZeoR-marked, TRP2-integrating Pichia pastoris roll-in expression plasmid, each as part of separate AOX1-driven expression cassettes containing the Saccharomyces cerevisiae alpha factor pre signal sequence (Seq ID NO: 3) to generate plasmid pGLY5883 (
Plasmids pGLY10044-10051, constructed by Genewiz (South Plainfield, N.J.), are derived from plasmid pGLY5883 and differ only by the indicated non-native N-glycosylation site introducing mutations in the anti-HER2 H chain cassette (Table 1) resulting in SEQ ID NO: 4-11.
Each of these plasmids was transformed into strain YGLY30329, a glycoengineered strain of P. pastoris that has been genetically engineered to produce N-glycans of the human complex type with terminal galactose acid residues (
Representative clones from the seven constructs that yielded fully folded antibody were cultivated in an Applikon (Foster City, Calif.) micro24 5 ml mini-fermenter apparatus. Seed cultures were prepared by inoculating strains from YSD plates to a Whatman 24-well Uniplate (10 ml, natural polypropylene) containing 3.5 ml of 4% BMGY medium (Invitrogen, Carlsbad, Calif.) buffered to pH 6.0 with potassium phosphate buffer. The seed cultures were grown 65-72 hours in a temperature controlled shaker at 24° C. and 650 rpm agitation. 1.0 ml of the 24 well plate grown seed culture and 4.0 ml of 4% BMGY medium was then used to inoculate each well of a Micro24 plate (Type: REG2). 30 ml of Antifoam 204 (1:25 dilution, Sigma Aldrich) was added to each well. The Micro24 was operated in Microaerobic1 mode and the fermentations were controlled at 200% dissolved oxygen, pH at 6.5, temperature at 24° C. and agitation at 800 rpm. The induction phase was initiated upon observance of a dissolved oxygen (DO) spike after the growth phase by adding bolus shots of methanol feed solution (100% [w/w] methanol, 5 mg/l biotin and 12.5 ml/l PTM2 salts), 50p in the morning and 125 μl in the afternoon. After approximately 72 hours of methanol induction, the cell-free culture supernatant was harvested by centrifugation at 2500× g in a Beckman swinging bucket centrifuge and subjected to protein A purification by standard methods (Jiang, 2011).
Antibody was quantified by reverse phase HPLC (Barnard et al, 2010) and also analyzed by capillary electrophoresis as described above, in this case both under non-reduced and reduced conditions. In all cases upon analysis using the Caliper LabChip GX software version 4.1, the selected clones produced protein consistent with well-assembled antibody, and consisting of a single heavy and light chain band in the reducing condition (
The protein was further subjected to Quadrapole Time-of-Flight Liquid chromatography/Mass spectrometry (Q-ToF mass spectrometry or Q-ToF LCMS or Q-ToF MS) analysis under reduced conditions as described previously (Lynaugh et al, 2013). Briefly, 5 μl (1 mg/ml) was injected in an Agilent Q-TOF 6520 mass spectrometer. The dual ESI ion source was set as follows: gas temp at 350° C.; drying gas at 13 L/min; nebulizer at 45 psig; fragmentor at 150 V; skimmer at 65 V; Oct1 RF VPP at 750 V; Vcap at 3500 V. Data were analyzed using MassHunter software. Of the seven constructs that were tested, six resulted in proteins where the second engineered N-glycan site was occupied with a glycan in addition to the canonical N-297 site (
Therefore, based on this evidence, it is not possible to simply select a site and introduce an Asn-turn sequence through mutagenesis that will lead to a well-folded protein and be efficiently N-glycan occupied.
Example 3: Bioreactor Expression and Purification of Non-Native N-Glycosylation Site Engineered Anti-HER2 AntibodyRepresentative clones from the six constructs that yielded fully folded antibody with a well-occupied non-native N-glycosylation site (See Table 1) were cultured in 1 L Fedbatch Pro fermenters (DASGIP Biotools, Shrewsbury, Mass.) using a glycerol fedbatch and methanol induction similarly to what has been described previously (Hopkins, 2011), with the notable difference of using a dissolved oxygen (DO) limited fed-batch induction paradigm. Briefly, inocula derived from yeast patches (isolated from a single colony) on agar plates were cultivated in 0.5 L baffled seed flasks in 0.1 L of 4% BSGY (without maltitol, table 2). Seed flasks were grown at 180 rpm and 24° C. (Innova 44, New Brunswick Scientific) for 48 hours. Bioreactor vessels were charged with 0.6 L of 0.2 μm filtered 4% BSGY media (plus 4 drops/L Sigma 204 antifoam, Table 2) and autoclaved at 121° C. for 45 minutes.
After sterilization and cooling, the aeration, agitation, and temperatures were set to 0.7 vvm, 600 rpm, and 24° C. respectively. The pH was adjusted to and controlled at 6.5 using 15% ammonium hydroxide. Inoculation of a prepared bioreactor occurred aseptically with 60 mL from a seed flask. Agitation was ramped to maintain 20% DO saturation. After the initial glycerol charge was consumed, denoted by a sharp increase in the DO, a 50% w/w glycerol solution containing 5 mg/L biotin and 32.3 mg/L PMTi4 was triggered to feed at 7.7 g/L-h for 8 hours. During the glycerol fed-batch phase 0.42 mL of PTM2 salts (Table 2) was injected manually. After completion of the glycerol fed-batch phase, the agitation rate was locked at 600 rpm and a bolus addition of 6.0 g of methanol containing 5 mg/L biotin and 12.5 mL/L PTM2 salts was added. During methanol induction phase the DO remains near 0% until the methanol bolus is entirely consumed. Each time the DO increases to >30% another 6.0 g bolus of the methanol feed solution is added to prolong the induction time. After methanol adaptation, it takes on average 9-10 hours to consume the 1% methanol boluses. Injections of 0.25 mL of 2.1 mg/mL PMTi4 (in methanol) were added each 24 hours of induction time. After 80-90 hours of methanol induction, the cell-free culture supernatant was harvested by centrifugation (Sorvall Evolution RC, Thermo Scientific) at 8500 rpm for 40 minutes and then subjected to small scale protein A purification by standard methods (Jiang, 2011).
Antibody was quantified by reverse phase TIPLC and calculated on a per liter basis (Barnard et al, 2010). Fermentation titers indicated that the N-glycan sites that were occupied and tolerated by the mAb structure based on small scale expression resulted in no significant alteration in mAb titer at 1 L fermentation scale (Table 3).
The purified antibody was further subjected to capillary electrophoresis and Q-ToF mass spectrometry analysis as outlined above. As with smaller scale cultivation, the selected clones produced protein consistent with well-assembled antibody, and consisting of a single heavy and light chain band in the reducing condition (
Larger aliquots (500 ml) of fermentation supernatant were purified by protein A chromatography for one each of the five best mutations (Samples D133202, D133203, D133208, D133404, and D133406, Table 3). The quantification of purified protein as measured by Bradford assay agreed well with the HPLC measurements from supernatant (Table 3). Purified protein was analyzed by Q-ToF and revealed masses that correspond to the expected L chain mass and several clustered masses that corresponded to the expected H chain mass (
To determine whether incorporation of non-canonical N-glycans into the anti-Her2 mAb sequence impacts binding of the antibody to the Her2 protein, the affinity of purifiedN-glycan modified mAbs was measured by surface plasmon resonance using a Biacore T-100 instrument (GE Healthcare, Little Chalfont, UK). First, a Series S CM5 Chip (GE Healthcare) was immobilized via amine coupling kit (GE Healthcare) to >10000 RU with an anti-human Fc capture antibody kit (GE Healthcare). Purified anti-Her2 antibody protein samples from batches D133202, D133203, D133404, and D133406 along with the commercial (CHO-produced trastuzumab) anti-Her2 were were captured to 30 RU on the active flowcells and no antibody was captured on the reference flowcell. Serially diluted human Her2 ectodomain (Biotang, Lexington, Mass.), ranging in concentration from 50 nMto 0.39 nM, was injected for 5 minutes over all flowcells and dissociation was monitored for 10 minutes. Binding data was double referenced by subtracting the reference flowcell signal and a 0 nM Her2 injection. All of the reagents were prepared in 1× HBS-EP+(GE Healthcare, pH7.4) running buffer and the binding measurements were performed on a Biacore T100 at 25° C. All data was fit with 1:1 Binding Model in Biacore T100 Evaluation Software (v2.0.4). Analysis of the binding curves, maximum binding capacity, and affinity, based on a 1:1 binding fit revealed no significant differences between commercial anti-Her2, trastuzumab (
Next, we asked whether N-glycans at non-native N-glycosylation sites on mAbs would be appropriate substrates and locales for chemical conjugation. Galactose oxidase (d-galactose:oxygen 6-oxidoreductase GO; EC 1.1.3.9) fromFusariumgraminarium, aka Dactylium dendroides (Fg GO) is a glycan-modifying enzyme previously shown to oxidize terminal β-1,4-galactose residues in the context of a protein (Cooper et al, 1959). The result of this enzymatic galactose oxidation is a chemically reactive aldehyde group that is receptive to direct conjugation with an alkoxyamine substrate to form a stable oxime bond (Ramya et al, 2013). However, attempts to oxidize and efficiently conjugate to the asialylated complex Fc N-297 glycan of a standard IgG, which typically contains a small but significant amount of terminal β-1,4-linked galactose (20-40% on one arm, 1-10% on both arms), have beenunsuccessful to date; a finding that was recapitulated here with commercial trastuzumab (
For non-native N-glycosylation site containing mAbs produced in GFI6.0 glycoengineered strains (
Conjugation reactions were next carried out with chemical catalysts for the two most receptive acceptor position anti-Her2 muteins (S134N and G161T). Initially, three different catalysts were used: 2-Amino-5-methoxybenzoic acid (AMB), 3,5-diaminobenzoic acid (DAB), and aniline (Crisalli 2013). Both aniline and AMB improved the conjugation efficiency, whereas addition of DAB did not result in increased conjugation. The conjugation reaction was improved most by the presence of 50 mM Aniline which, after 72 h resulted in >90% of the available terminal galactose residues having a fluorophore (
Using these optimized conditions, conjugation reactions were carried out for each of the five purified modified mAbs containing non-native N-glycosylation sites (N206T, V363T, Q438N, S134N, and G161T). The glycan modified antibodies were conjugated with alkoxyamine-modified Alexafluor488 fluorophore (Alexa488, Invitrogen, Claremont, Calif.). Conjugation proceeded highly efficiently for 4 of the 5 with a significant proportion of singly conjugated H chain remaining for the N203T variant. However, even for this protein the plurality of resulting mAb contained two conjugated fluorophores (
The minor conjugation of a 3rd site observed for three of the glycan modified mAbs (N206T, V363T, and Q438N), can be interpreted based on mass to be conjugation of the N-297 glycan on hybrid galactosylated (GS3.5,
Taken together, these data demonstrate that nearly quantitative oxime conjugation can be achieved at certain non-native N-glycosylation sites of glycan modified mAbs following enzymatic oxidation of galactose residues to a reactive aldehyde form. Moreover, even under conditions that promote highly efficient conjugation to the desired site, no non-specific oxidation or conjugation is observed. Finally under these conditions, complex N-glycans at the N-297 of the Fc (a modest fraction of which are galactosylated GS4.5 and GS5.0) are not oxidized by the GalOx enzyme, thereby maintaining site-specificity of the conjugation reaction irrespective of the presence of a complex glycan at the canonical N-297 site. Thus, importantly, this glycan-based conjugation is completely compatible with full effector function-enabled antibodies.
Example 8: Scale-Up and Bioanalytical Characterization of Glyco-Conjugated AbsThe conjugation reaction described in Example 5 (modified by addition of aniline as described in Example 7) was scaled to larger volume using the S134N and G161T modified anti-Her2 mAb sequences. Alkoxyamine-modified Alexa488 and alkoxyamine modified biotin were used as conjugation substrates (100 mM for each) and conjugation reactions were carried out at 25° C. for 72 h. The reaction products were subjected to Q-ToF MS with the results shown in
The Alexa488 conjugated G161T glycan modified anti-Her2 antibody was also subjected to IdeS (Fabricator, NEB, Ipswich, Mass.) digestion and Q-ToF MS to confirm the location of the conjugated dye. The IdeS digestion was carried out according to the manufacturer's instructions. Upon digestion and MS analysis, it was observed that the two non-native N-glycosylation sites residing on the F(ab′)2 were modified with 3-4 Alexa 488 moieties while the Fc-fragment was nearly completely unmodified.
The same Alexa488 conjugated G161T glycan modified anti-Her2 antibody (
In order to further probe stability, the glycan-modified antibodies were incubated at 45° C. for 2 weeks in 100 mM sodium phosphate pH 7.0 at a concentration of 5 mg/ml and then subjected to SEC. All samples retained intactness and resisted aggregation except for the G161T modified antibody, which degraded slightly more rapidly at 45° C. than the commercial control or other glycan-modified mAbs (
An aminooxy chemically activated Exendin-4 peptide modified at the gamma amine of the C-terminal Lysine (
An aminooxy activated C5-linker containing DM1 (alkoxy-C5-DM1,
With the knowledge that combined enzymatic/chemical conjugation can occur efficiently at selected engineered N-glycan sequons a further set of native N-glycosylation sites were constructed by introducing site-directed mutants into an IgG to determine whether these new structurally selected sites would be suitable substrates for 1) efficient addition of N-glycans and 2) conjugation of cargo. A list of mutations that were constructed and the associated sequence references is found in Table 4.
Notably, at some sites more than a single mutation was required to generate an efficient predicted NXS/T (where X is not Pro) sequon. Mutations were introduced into the anti-Her2 IgG1 mAb sequence in plasmid pGLY5883 (
The S134N and G161T mutations provide two efficient N-glycan sites for conjugation (N134 and N159). We next sought to determine if these sites could be combined on the same antibody scaffold to generate an ADC with a DAR:8 at specific sites of conjugation. The S134N mutated anti-Her2 antibody was mutated to incorporate G161T or G161S mutations. The resulting plasmids (pGLY14135 and pGLY14136) were transformed into strain YGLY30329 as described in Example 2. Two resulting clones of each were cultivated in Dasgip 1 L fermenters as described in Example 3. The fermentation supernatant was purified by protein A chromatography and the resulting protein subjected to Q-ToF analysis. Both the S134N/G161T and S134N/G161S double mutein containing mAbs were efficiently glycosylated at 3 sites on each reduced H chain (N134, N159, and N297) with minimal residual singly or doubly glycosylated protein (
Given that Abs can be produced accommodating two N-glycan sites and the glycoengineered yeast system can modify these sites efficiently to terminal galactose (Illustrated in
Plasmids pGLYl4172-14179, constructed by Genewiz (South Plainfield, N.J.), contain the null-Her2 H and L chain sequences as derived from pGLY11576 (
Each of these plasmids was transformed into strain YGLY30329 and clones were selected and screened for secretion of antibody in 96 DWP format as described in Example 1. Following this, several positive clones were cultivated in 5 ml micro24 reactors and the supernatants were harvested by centrifugation and purified by protein A chromatography as described in example 2 above. The purified samples were subjected to capillary electrophoresis (CE) on a Labchip GXII instrument (Caliper Life Sciences, Hopkinton, Mass.) using the standard HT Protein Express 200 method as described (Gomathinayagam, 2012). From this analysis it was possible to conclude that most of the additional N-glycosylation sites were indeed occupied due to the shifts in migration. To illustrate this, a single representative purified non-reduced CE sample from each of the plasmids was displayed using the Labchip GXII visualization software version 4.1 (
Several clones from strain YGLY30329 expressing plasmids pGLY14172-14179 were cultivated in Dasgip IL fermenters as described in Example 3 above. Following around 80-90 h of methanol induction, supernatants were harvested by centrifugation and purified by standard protein A chromatography (Example 3 above and Jiang, 2011). The purified Abs from these strains were then subjected to Q-ToF MS under reducing conditions (see example 2 above). The results, illustrated in
In addition to generating highly glycan-modified Abs with terminal galactose for conjugation purposes, it could be desirable to produce antibodies with a high degree of sialylation in the same manner. Such Abs could be used for conjugation by chemical modification of the sialic acid residues (Ramya, 2013).
To generate mAbs with a high degree of sialylation, the plasmids illustrated in Example 12 (see table 5) were transformed into Glycoengineered Pichia strain YGLY36472 capable of modifying secreted proteins with the biantennary sialylated human N-glycan (see, e.g., Hamilton, 2006;
To assure that the efficient modification of the anti-HER2 antibody with non-canonical N-glycans is not restricted to the anti-HER2 sequence we modified additional mAb sequences with different antigen-binding Fab regions. A pair (H and L) of variable domain sequences directed against the murine Programmed Cell Death 1 (PD-1) ligand was constructed as a human IgG1 chimera (Seq ID 42 and 43). This chimeric mAb sequence was further modified to incorporate the S134N (EU, Seq ID 44) or G161T (EU, Seq ID 45) mutations, which each add one additional N-glycan to the CHi domain or the combined S137N/G161T mutations (EU, Seq ID 46), which adds two additional N-glycans per H chain. The original anti-mPD-1 H chain sequence (pGLY13649,
In addition to the anti-mPD-1 Ab sequence, an anti-CS1 Ab sequence H chain and L chain (Zha 2013, Seq ID 47 and Seq ID 48, respectively) was modified to incorporate the same sets of mutations, S134N (EU, Seq ID 49), G161T (EU, Seq ID 50), and the double mutant S134N/G161T (EU, Seq ID 51). The original anti-CS-1 H chain sequence (pGLY8040,
Finally, a previously published anti-CD70 antibody sequence (Coccia, USapp 2010/0150950 A1) was modified to incorporate the same sets of mutations, S134N (EU), G161T (EU), and the double mutant (S134N/G161T). The anti-CD70 VH and VL sequences (Seq ID 52 and 53, respectively) were synthesized and constructed by Genewiz (South Plainfield, N.J.) in a human IgG1 frameworkby cloning into plasmid pGLY5730 (
Claims
1. An engineered IgG antibody or heavy chain constant domain fragment comprising
- an S134N mutation in the heavy chain constant domain, which forms a first non-native N-glycosylation site having the amino acid sequence NTS over positions 134-136 of the heavy chain constant domain and a G161T or G161S mutation, which forms a second non-native N-glycosylation site in the heavy chain constant domain having the amino acid sequence NST over positions 159-161 of the heavy chain constant domain, said non-native N-glycosylation sites having an N-glycan attached to the N at position 134 and 159, wherein the N-glycans have a Gal2GlcNAc2Man3GlcNAc2 or GalGlcNAcMan3GlcNAc2 glycoform in which the terminal galactose residues have been oxidized to a C-6 aldehyde group, which is conjugated to a reactive amine group of a derivatized drug by oxime bonds, and wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
2. An engineered IgG antibody or heavy chain constant domain fragment of claim 1, wherein N-glycan comprises a Gal2GlcNAc2Man3GlcNAc2 glycoform.
3. An engineered IgG antibody or heavy chain constant domain fragment of claim 1, wherein N-glycan comprises a Gal2GlcNAc2Man3GlcNAc2 glycoform.
4. An engineered IgG antibody or heavy chain constant domain fragment of claim 1, wherein the engineered IgG antibody or heavy chain constant domain fragment further comprises one to ten amino acid mutations or pairs of mutations are selected from the group consisting of N203 T, N203S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
5. An engineered IgG antibody or heavy chain constant domain fragment of claim 1, wherein the derivatized drug is selected from the group consisting of a polymer, cytotoxic agent, a radionuclide, fluorescent or chemiluminescent labels, steroid, steroid receptor agonist, signal transduction inhibitor, a peptide and scFv.
6. An engineered IgG antibody or heavy chain constant domain fragment of claim 1, wherein the derivatized drug comprises a cytotoxic agent.
7. The engineered IgG antibody or antigen binding fragment of claim 1, wherein the IgG antibody further comprises one or two N-glycosylation sites in the variable domain that have been generated by amino acid mutations selected from the group consisting of Q105N and S113N, wherein the numbering is according to the Kabat numbering system.
8. The engineered IgG antibody or constant domain fragment of claim 1, wherein the IgG antibody is selected from the group consisting of anti-Her2, anti-Her2/neu, anti-glycoprotein IIb/IIIa, anti-TNF-α, anti-CD52, anti-CD25, anti-BAFF, anti-Vascularendothelial growth factor, anti-CD30, anti-IL-1β, anti-epidermal growth factor receptor, anti-RANK Ligand, anti-Complement C5, anti-CD11a, anti-CD33, anti-CD20, anti-CTLA-4, anti-T cell CD3 Receptor, anti-α-4 (α4) integrin, anti, anti-Immunoglobulin E, anti-RSV F protein, anti-epidermal growth factor receptor, anti-VEGF-A, anti-ErbB2, anti-IL-12/IL-23, anti-integrin α4β7, anti-CD274, anti-3-amyloid, anti-4-1BB, anti-SAC, anti-5T4, anti-ACVR2B, anti-adenocarcinomaantigen, anti-AGS-22M6, anti-α-fetoprotein, anti-angiopoietin 2, anti-angiopoietin 3, anti-anthrax toxin, anti-AOC3, anti-, anti-B7-H3, anti-Bacillus anthracia, anti-β amyloid, anti-B-lymphoma cell, anti-C242 antigen, anti-05, anti-CA-125, anti-carbonic anhydrase 9, anti-cardiac myosin, anti-CCL11, anti-CCR4, anti-CCR5, anti-CD11/CD18, anti-CD125, anti-CD140a, anti-CD147, anti-CD15, anti-CD152, anti-CD154, anti-CD19, anti-CD2, anti-CD200, anti-CD22, anti-CD221, anti-CD23, anti-CD27, anti-CD28, anti-CD3, anti-CD3 epsilon, anti-CD30, anti-CD37, anti-CD38, anti-CD4, anti-CD40, anti-CD41, anti-CD44, anti-CD5, anti-CD51, anti-CD52, anti-CD56, anti-CD6, anti-CD70, anti-CD74, anti-CD79B, anti-CD80, anti-CEA, anti-CFD, anti-ch4D5, anti-CLDN18.2, anti-C. difficile, anti-clumping factor A, anti-CSF2, anti-cytomegalovirus, anti-CMV gp B, anti-DLL4, anti-DRS, anti-E. coli shiga toxin type-1 or 2, anti-EGFL7, anti-endotoxin, anti-EpCAM, anti-EpCAM/CD3, anti-episialin, anti-ERBB3, anti-Escherichia coli, anti-F protein, anti-FAP, anti-fibrin II, anti-βchain, anti-fibronectin extra domain-B, anti-folate receptor 1, anti-Frizzled receptor, anti-GD2 ganglioside, anti-GD3 ganglioside, anti-GMCSF receptor α-chain, anti-GPNMB, anti-Influenza, anti-Influenza hemagglutinin, anti-hepatitis B, anti-surface antigen, anti-HER1, anti-HER3, anti-HGF, anti-HHGFR, anti-HIV-1, anti-HLA-DR, anti-HNGF, anti-Hsp90, anti-human scatter factor receptor kinase, anti-human TNF, anti-human β-amyloid, anti-CD54, anti-IFN-α, anti-IFN-γ, anti-IgE Fc region, anti-IGF-1 receptor, anti-IGF-I, anti-IgG4, anti-IGHE, anti-IL-13, anti-IL-17, anti-IL-17A, anti-IL-10, anti-IL-22, anti-IL-23, anti-IL-4, anti-IL-5, anti-IL-6, anti-IL-6 receptor, anti-IL9, anti-ILGF2, anti-insulin-like growth factor I receptor anti-integrin α4, anti-integrin α5β1, anti-integrin α7β7, anti-integrin αIIbβ3, anti-integrin αvβ3, anti-interferon receptor, anti-interferon α/β receptor, anti-interferon γ-induced protein, anti-ITGA2, anti-KIR2D, anti-Lewis-Y antigen, anti-lipoteichoic acid, anti-LOXL2, anti-L-selectin (CD62L), anti-LTA, anti-MCP-1, anti-mesothelin, anti-MS4A1, anti-MUC1, anti-mucin CanAg, anti-myostatin, anti-NARP-1, anti-NCA-90, anti-NGF, anti-N-glycolylneuraminic acid, anti-NOGO-A, anti-Notch receptor, anti-NRP1, anti-Oryctolagus cuniculus, anti-OX-40, anti-oxLDL, anti-PCSK9, anti-PD-1, anti-PDCD1, anti-PDGF-R α, anti-phosphate-sodium co-transporter, anti-phosphatidylserine, anti-prostatic carcinoma cells, anti-Pseudomonas aeruginosa, anti-rabies virus, anti-rabies virus glycoprotein, anti-respiratory syncytial virus, anti-RHD, anti-Rhesus factor, anti-RON, anti-RTN4, anti-sclerostin, anti-SDC1, anti-selectin P, anti-SLAMF7, anti-SOST, anti-sphingosine-1-phosphate, anti-TAG-72, anti-T-cell receptor, anti-TEM1, anti-tenascin C, anti-TFPI, anti-TGFβ1, anti-TGFβ2, anti-TGF-β, anti-TRAIL-R1, anti-TRAIL-R2, anti-tumor antigen CTAA16.88, anti-TWEAK receptor, anti-TYRP1, anti-VEGF-A, anti-VEGFR-1, anti-VEGFR2, anti-vimentin, anti-VWF, anti-IL-1, anti-IL-2, anti-IL-5, anti-IL-8, anti-IL-12, anti-IL-15, anti-IL-18, anti-IL-20, anti-IL-21, anti-IL-23R, anti-IL-25, anti-IL-27, anti-IL-33, anti-CD14, anti-CD18, anti-CD64, anti-CD200, anti-CD200R, anti-TSLP, anti-TSLPR, anti-PDL1, anti-VLA-4, anti-E-selectin, anti-Fact II, anti-ICAM-3, anti-β2-integrin, anti-CBL, anti-LCAT, anti-CR3, anti-MDL-1, anti-GITR, anti-CGRP, anti-TRKA, anti-IGF1R, and anti-GTC.
9. The engineered IgG antibody or constant domain fragment of claim 1, wherein the IgG antibody is selected from the group consisting of abciximab, adalimumab, certolizumab pegol, golimumab, infliximab, alemtuzumab, basiliximab), belimumab, bevacizumab, brentuximab, canakinumab, cetuximab, daclizumab, denosumab, eculizumab, efalizumab, gemtuzumab, ibritumomab tiuxetan, ipilimumab, muromonab-cd3, natalizumab, ofatumumab, omalizumab, palivizumab, panitumumab, ranibizumab, rituximab, tocilizumab, atlizumab, tositumomab, trastuzumab, ustekinumab, and vedolizumab.
10. A method of preparing a conjugated N-glycosylated IgG antibody or fragment thereof comprising an N-glycan attached to the N at position 134, wherein the N-glycan has a Gal2GlcNAc2Man3GlcNAc2 or GalGlcNAcMan3GlcNAc2 glycoform in which the terminal galactose residues are conjugated to a reactive amine group of a derivatized drug by an oxime bond, the method comprising:
- (a) transforming a yeast or filamentous fungus host cell genetically engineered to produce N-glycans comprising terminal galactose residues of the structure Gal(1-4)GlcNAc(1-4)Man3GlcNAc2 or the structure Gal(1-2)GlcNAc(1-2)Man5GlcNAc2 with a nucleic acid encoding an IgG heavy chain constant domain having the amino acid sequence NTS over positions 134-136 of the heavy chain constant domain;
- b) culturing the transformed host cell under conditions that allow the expression of the IgG heavy chain constant domain comprising terminal galactose residues;
- (c) contacting the expressed IgG heavy chain constant domain with a reagent that oxidizes the terminal galactose residues to a C-6 aldehyde group; and
- (d) conjugating the reactive amine group of a derivatized drug to the C-6 aldehyde group to produce the conjugated N-glycosylated IgG antibody or fragment thereof, wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
11. The method of claim 10, wherein the IgG heavy chain further comprising a G161 T mutation, which forms a second non-native N-glycosylation site in the heavy chain constant domain having the amino acid sequence NST over positions 159-161 of the heavy chain constant domain, wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
12. The method of claim 10, wherein the engineered IgG antibody or heavy chain constant domain fragment further comprises one to ten amino acid mutations or pairs of mutations are selected from the group consisting of N203 T, N203 S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K2l10T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423 T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, whereinthe amino acid positions of the heavy chain contant domain are according to Eu numbering.
13. The method of claim 10, wherein the nucleic acid encodes an IgG antibody and further comprises one or two N-glycosylation sites in the variable domain that have been generated by amino acid mutations selected from the group consisting of Q105N and S113N, wherein the numbering is according to the Kabat numbering system.
14. The method of claim 11, wherein the engineered IgG antibody or heavy chain constant domain fragment further comprises one to ten amino acid mutations or pairs of mutations are selected from the group consisting of N203 T, N203 S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, andG194N/Q196S, wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
15. The method of claim 11, wherein the nucleic acid encodes an IgG antibody and further comprises one or two N-glycosylation sites in the variable domain that have been generated by amino acid mutations selected from the group consisting of Q105N and S113N, wherein the numbering is according to the Kabat numbering system.
16. The method of claim 10, wherein the yeast host cell is selected from the group consisting of Pichia pastoris (Komagataella pastoris), Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichiathermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia minuta (Ogataea minuta, Pichia lindneri), Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorphs, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichodermareesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, and Neurospora crassa.
17. An engineered IgG antibody or heavy chain constant domain fragment comprising
- a G161 T mutation, which forms a second non-native N-glycosylation site in the heavy chain constant domain having the amino acid sequence NST over positions 159-161 of the heavy chain constant domain, said non-native N-glycosylation site having an N-glycan attached to the N at position 134, wherein the N-glycan has a Gal2GlcNAc2Man3GlcNAc2 glycoform or GalGlcNAcMan3GlcNAc2 glycoform in which the terminal galactose residues have been oxidized to a C-6 aldehyde group, which is conjugated to a reactive amine group of a derivatized drug by an oxime bond, and wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
18. The engineered IgG antibody or constant domain fragment of claim 17, wherein the engineered IgG antibody or heavy chain constant domain fragment further comprises one to ten amino acid mutations or pairs of mutations are selected from the group consisting of N203 T, N203S, V363T, V363S, Q438N, S176N, A118N, S132N, K133N, A162N, T195N, K210T, Y391T, F423T, F423S, Y436T, Y436S, L193N, K392T, K392S, F423T, S176N/G178T, S176N/G178S, Q419N/N421T, Q419N/N421S, S191N/L193T, S191N/L193S, G194N/Q196T, and G194N/Q196S, wherein the amino acid positions of the heavy chain contant domain are according to Eu numbering.
19. The engineered IgG antibody or constant domain fragment of claim 17, wherein the IgG antibody and further comprises one or two N-glycosylation sites in the variable domain that have been generated by amino acid mutations selected from the group consisting of Q105N and S113N, wherein the numbering is according to the Kabat numbering system.
20. The engineered IgG antibody or constant domain fragment of claim 17, wherein the IgG antibody is
- (a) selected from the group consisting of anti-Her2, anti-Her2/neu, anti-glycoprotein IIb/IIIa, anti-TNF-α, anti-CD52, anti-CD25, anti-BAFF, anti-Vascularendothelial growth factor, anti-CD30, anti-IL-1β, anti-epidermal growth factor receptor, anti-RANK Ligand, anti-Complement C5, anti-CD11a, anti-CD33, anti-CD20, anti-CTLA-4, anti-T cell CD3 Receptor, anti-α-4 (a4) integrin, anti, anti-Immunoglobulin E, anti-RSV F protein, anti-epidermal growth factor receptor, anti-VEGF-A, anti-ErbB2, anti-IL-12/IL-23, anti-integrin α407, anti-CD274, anti-3-amyloid, anti-4-1BB, anti-SAC, anti-5T4, anti-ACVR2B, anti-adenocarcinomaantigen, anti-AGS-22M6, anti-α-fetoprotein, anti-angiopoietin 2, anti-angiopoietin 3, anti-anthrax toxin, anti-AOC3, anti-, anti-B7-H3, anti-Bacillus anthracia, anti-β amyloid, anti-B-lymphoma cell, anti-C242 antigen, anti-05, anti-CA-125, anti-carbonic anhydrase 9, anti-cardiac myosin, anti-CCL11, anti-CCR4, anti-CCR5, anti-CD11/CD18, anti-CD125, anti-CD140a, anti-CD147, anti-CD15, anti-CD152, anti-CD154, anti-CD19, anti-CD2, anti-CD200, anti-CD22, anti-CD221, anti-CD23, anti-CD27, anti-CD28, anti-CD3, anti-CD3 epsilon, anti-CD30, anti-CD37, anti-CD38, anti-CD4, anti-CD40, anti-CD41, anti-CD44, anti-CD5, anti-CD51, anti-CD52, anti-CD56, anti-CD6, anti-CD70, anti-CD74, anti-CD79B, anti-CD80, anti-CEA, anti-CFD, anti-ch4D5, anti-CLDN18.2, anti-C. difficile, anti-clumping factor A, anti-CSF2, anti-cytomegalovirus, anti-CMV gp B, anti-DLL4, anti-DRS, anti-E. coli shiga toxin type-1 or 2, anti-EGFL7, anti-endotoxin, anti-EpCAM, anti-EpCAM/CD3, anti-episialin, anti-ERBB3, anti-Escherichia coli, anti-F protein, anti-FAP, anti-fibrin II, anti-β chain, anti-fibronectin extra domain-B, anti-folate receptor 1, anti-Frizzled receptor, anti-GD2 ganglioside, anti-GD3 ganglioside, anti-GMCSF receptor α-chain, anti-GPNMB, anti-Influenza, anti-Influenza hemagglutinin, anti-hepatitis B, anti-surface antigen, anti-HER1, anti-HER3, anti-HGF, anti-HHGFR, anti-HIV-1, anti-HLA-DR, anti-HNGF, anti-Hsp90, anti-human scatter factor receptor kinase, anti-human TNF, anti-human β-amyloid, anti-CD54, anti-IFN-α, anti-IFN-γ, anti-IgE Fc region, anti-IGF-1 receptor, anti-IGF-I, anti-IgG4, anti-IGHE, anti-IL-13, anti-IL-17, anti-IL-17A, anti-IL-10, anti-IL-22, anti-IL-23, anti-IL-4, anti-IL-5, anti-IL-6, anti-IL-6 receptor, anti-IL9, anti-ILGF2, anti-insulin-like growth factor I receptor, anti-integrin α4, anti-integrin α5β1, anti-integrin α7β7, anti-integrin αIIbβ3, anti-integrin αvβ3, anti-interferon receptor, anti-interferon α/β receptor, anti-interferon 7-induced protein, anti-ITGA2, anti-KIR2D, anti-Lewis-Y antigen, anti-lipoteichoic acid, anti-LOXL2, anti-L-selectin (CD62L), anti-LTA, anti-MCP-1, anti-mesothelin, anti-MS4A1, anti-MUC1, anti-mucin CanAg, anti-myostatin, anti-NARP-1, anti-NCA-90, anti-NGF, anti-N-glycolylneuraminic acid, anti-NOGO-A, anti-Notch receptor, anti-NRP1, anti-Oryctolagus cuniculus, anti-OX-40, anti-oxLDL, anti-PCSK9, anti-PD-1, anti-PDCD1, anti-PDGF-R α, anti-phosphate-sodium co-transporter, anti-phosphatidylserine, anti-prostatic carcinoma cells, anti-Pseudomonas aeruginosa, anti-rabies virus, anti-rabies virus glycoprotein, anti-respiratory syncytial virus, anti-RHD, anti-Rhesus factor, anti-RON, anti-RTN4, anti-sclerostin, anti-SDC1, anti-selectin P, anti-SLAMF7, anti-SOST, anti-sphingosine-1-phosphate, anti-TAG-72, anti-T-cell receptor, anti-TEM1, anti-tenascin C, anti-TFPI, anti-TGFβ1, anti-TGFβ2, anti-TGF-β, anti-TRAIL-R1, anti-TRAIL-R2, anti-tumor antigen CTAA16.88, anti-TWEAK receptor, anti-TYRP1, anti-VEGF-A, anti-VEGFR-1, anti-VEGFR2, anti-vimentin, anti-VWF, anti-IL-1, anti-IL-2, anti-IL-5, anti-IL-8, anti-IL-12, anti-IL-15, anti-IL-18, anti-IL-20, anti-IL-21, anti-IL-23R, anti-IL-25, anti-IL-27, anti-IL-33, anti-CD14, anti-CD18, anti-CD64, anti-CD200, anti-CD200R, anti-TSLP, anti-TSLPR, anti-PDL1, anti-VLA-4, anti-E-selectin, anti-Fact II, anti-ICAM-3, anti-02-integrin, anti-CBL, anti-LCAT, anti-CR3, anti-MDL-1, anti-GITR, anti-CGRP, anti-TRKA, anti-IGF1R, and anti-GTC; or
- (b) selected from the group consisting of abciximab, adalimumab, certolizumab pegol, golimumab, infliximab, alemtuzumab, basiliximab), belimumab, bevacizumab, brentuximab, canakinumab, cetuximab, daclizumab, denosumab, eculizumab, efalizumab, gemtuzumab, ibritumomab tiuxetan, ipilimumab, muromonab-cd3, natalizumab, ofatumumab, omalizumab, palivizumab, panitumumab, ranibizumab, rituximab, tocilizumab, atlizumab, tositumomab, trastuzumab, ustekinumab, and vedolizumab.
Type: Application
Filed: Apr 11, 2022
Publication Date: Aug 4, 2022
Applicant: Merck Sharp & Dohme Corp. (Rahway, NJ)
Inventors: Robert Davidson (Enfield, NH), Bing Gong (North Reading, MA)
Application Number: 17/658,731
