Patent Grant
11845970
The invention relates to glycoprotein synthesis, and more particularly, to the use of a recombinant mutants Endo S2, an Endo-β-N-acetylglucosminidase from the strain NZ131 of serotype M49 of Streptococcus pyogenes, that possesses transglycosylation activity and limited hydrolyzing activity thereby providing for efficient glycosylation remodeling of antibodies.
Monoclonal antibodies (mAbs) represent a major class of therapeutic proteins used for the treatment of cancers, inflammatory disorders, and infectious diseases [1-3]. Compelling experimental data have shown that glycosylation can have profound impacts on the stability, biological functions, and overall therapeutic efficacy of antibodies [4-7]. For example, core-fucosylation of Fc glycans could significantly reduce the antibody-dependent cellular cytotoxicity (ADCC), and antibodies with low content of core fucosylation have shown improved therapeutic efficacy in anti-cancer therapy [8,9]. On the other hand, it has been reported that the terminal α-2,6-sialylated Fc glycoform, a minor component in the intravenous immunoglobulin (IVIG), is responsible for the anti-inflammatory activity of IVIG as demonstrated in animal models [10-13]. However, natural and recombinant antibodies are usually produced as heterogeneous glycoforms that are difficult to separate for further probing the structure-activity relationships of antibodies. Moreover, for a majority of anti-cancer mAbs on the market that rely on ADCC as a major mechanism of the therapeutic efficacy, the most active non-fucosylated glycoforms are usually present as minor fractions among the heterogeneous mixtures [8,9]. Thus, methods that can lead to the production of structural well defined, homogeneous glycoforms of antibodies are highly desirable for both functional studies and for the development of better antibody-based therapeutics. In parallel to the attempt to control glycosylation through host glycosylation pathway engineering [14-20], a chemoenzymatic glycosylation remodeling method, which involves endoglycosidase-catalyzed deglycosylation and subsequent transglycosylation of intact antibodies, has been emerging as a promising approach to obtain homogeneous antibody glycoforms [21]. It has been shown that the Fc glycans of recombinant IgG-Fc domain could be remodeled through the enzymatic deglycosylation-transglycosylation steps under the catalysis of an appropriate endoglycosidase, including Endo-A and Endo-D, without the need of denaturing the proteins [22-24]. In 2012, the first example of glycosylation remodeling of an intact therapeutic monoclonal antibody and IVIG, which was enabled by the discovery of glycosynthase mutants of Endo-S, an endoglycosidase from Streptococcus pyogenes [25]. In this approach, the heterogeneous Fc glycans of a monoclonal antibody such as rituximab are removed by Endo S catalyzed deglycosylation to yield the antibody protein backbone carrying only the α1,6-fucosylated GlcNAc acceptor at the glycosylation site. Then a desired N-glycan is transferred to the GlcNAc acceptor by an Endo-S glycosynthase mutant (Endo S-D233A or D233Q) in a site- and stereo-specific manner to reconstitute a homogeneous glycoform of the antibody. The Endo-S glycosynthase mutants have been used by several research groups for the synthesis of different homogeneous glycoforms of antibodies for structural and functional studies [26-31]. While the Endo-S glycosynthases were able to transfer biantennary complex type and modified Man3GlcNAc core, these mutants showed only marginal activity in transferring high-mannose type N-glycans. More recently, glycosynthase mutants from Endo-F3 have been generated, another GH18 family endoglycosidase [32]. It was found that the Endo-F3 glycosynthases, such as the D165A mutant, was able to transfer triantennary N-glycan to Fc domain of intact antibody, but they required α1,6-fucosylated GlcNAc moiety as the acceptor for transglycosylation and were unable to transfer to non-fucosylated GlcNAc acceptors. These studies have demonstrated that the glycosynthases so far available still have limitations due to substrate specificity and also vary in transglycosylation efficiency.
With an understanding of the shortcomings of other mutants, an effort to expand the scope of the glycosylation remodeling strategy, is described herein wherein attention is turned to Endo-S2, an endoglycosidase from Streptococcus pyogenes of serotype M49 [33,34]. Endo-S2 shows only 37% sequence identity to Endo-S from the same bacteria and demonstrates a broader glycan substrate specificity in Fc deglycosylation than Endo-S [34]. Data implicated that the wild type Endo-S2 can hydrolyze various types of N-glycans from antibody Fc domains than Endo-S. But it has been unknown whether Endo-S2 possesses transglycosylation activity and, if yes, whether Endo-S2 glycosynthases can be generated by site-directed mutagenesis.
Thus, it would be advantageous to evaluate whether efficient glycosynthases could be generated from Endo-S2 and whether they would potentially have broader substrate specificity in transglycosylation than those previously reported.
The present invention provides for recombinant Endo-S2 mutants (named Endo-S2 glycosynthases) that exhibit reduced hydrolysis activity and increased transglycosylation activity for the synthesis of glycoproteins wherein a desired sugar chain is added to a fucosylated or nonfucosylated GlcNAc-IgG acceptor. As such, the present invention allows for the synthesis and remodeling of therapeutic antibodies thereby providing for certain biological activities, such as, prolonged half-life time in vivo, less immunogenicity, enhanced in vivo activity, increased targeting ability, and/or ability to deliver a therapeutic agent. The mutant Endo-S2 glycosynthases of the present enable the glycosylation remodeling of therapeutic antibodies and Fc fragments thereof with increase number of diverse glycans such as high-mannose type and hybrid type glycans that cannot be achieved by the previously disclosed Endo-S mutants.
In one aspect, the present invention provides for transglycosylation activity of mutants of an endo-β-N-acetylglucosamindase of strain NZ131 of serotype M49 of Streptococcus pyogenes (Endo-S2) (SEQ ID NO: 1), wherein the mutants have at least 85% homology thereto and exhibit transglycosylation activity on both fucosylated and nonfucosylated GlcNAc-IgG acceptors, wherein the endoglycosidases enable the transfer of an oligosaccharide (in the form of an activated sugar oxazoline) en bloc to a fucosylated or nonfucosylated GlcNAc-IgG to form a new glycoform of IgG.
In another aspect, the present invention provides for Endo-S2 mutant proteins that show remarkably enhanced transglycosylation efficiency and diminished or abrogated product hydrolytic activity relative to the wild type Endo S2. Mutants preferably include site-specific mutations including a mutation at Asp-184. The mutant proteins include, but are not limited to, D184A (SEQ ID NO: 2), D184N (SEQ ID NO: 3), D184Q (SEQ ID NO: 4), D184R (SEQ ID NO: 5), D184C (SEQ ID NO: 6), D184M (SEQ ID NO: 7), D184E (SEQ ID NO: 8), D184G (SEQ ID NO: 9), D184H (SEQ ID NO: 10), D184I (SEQ ID NO: 11), D184L (SEQ ID NO: 12), D184K (SEQ ID NO: 13), D184F (SEQ ID NO: 14), D184P (SEQ ID NO: 15), D184S(SEQ ID NO: 16), D184T (SEQ ID NO. 17); D184W (SEQ ID NO: 18), D184Y(SEQ ID NO: 19), D184V (SEQ ID NO: 20) or fragments thereof that include the catalytic domain and exhibit increased transglycosylation and reduced hydrolysis related to the wild type Endo-S2 protein. Preferably the mutant proteins include D184M (SEQ ID NO: 7), D184E (SEQ ID NO: 8) and D184Q (SEQ ID NO: 4).
Notably any Endo-S2 fragments and domains that carry a mutation at the D184 site are included in the present invention wherein any such domains and fragments may be fused to other proteins including, but not limited to, CPD, Fc, MBP, etc. The catalytic domain and the specific site of mutation are critical for the enzymatic activity, and thus, other sites on the enzyme may be modified or truncated, such as a terminus without affect much of the glycosynthase activity
In a further aspect, the present invention provides for a chemoenzymatic method for the preparation of a homogeneous fucosylated or nonfucosylated glycoforms of IgG antibodies, comprising:
a. providing an acceptor selected from the group consisting of a core fucosylated GlcNAc-IgG and nonfucosylated GlcNAc-IgG or corresponding IgG-Fc fragments; and
b. reacting the acceptor with a donor substrate including an activated oligosaccharide moiety, in the presence of a S. pyogenes Endo-S2 Asp-184 mutant protein or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme to transfer the activated oligosaccharide moiety to the acceptor and yield the homogeneous fucosylated or nonfucosylated glycoprotein.
In a still further aspect, the present invention provides a method for preparing a core-fucosylated IgG or IgG-Fc fragment having a predetermined oligosaccharide moiety, comprising:
a. providing a core-fucosylated acceptor protein comprising an asparagine-linked core-fucosylated N-acetylglucosamine (GlcNAc) residue; and
b. enzymatically reacting the core-fucosylated acceptor protein with an activated oligosaccharide donor in the presence of a Endoglycosidase-S2 D184 mutant protein or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme, wherein the activated oligosaccharide donor carries an oligosaccharide moiety comprising a predetermined number and type of sugar residues, wherein the oligosaccharide moiety is covalently linked to the acceptor protein, thereby preparing the core-fucosylated IgG or IgG-Fc fragment having the predetermined oligosaccharide moiety.
In yet another aspect, the present invention provides for an activated oligosaccharide moiety, such as glycan or oligosaccharide oxazoline, glycosyl fluoride, glycosyl azide or an aryl glycoside, as a donor substrate for the synthesis of homogeneous core-fucosylated glycoproteins or nonfucosylated glycoproteins. Preferably the activated oligosaccharide moiety is an oligosaccharide oxazoline.
In a further aspect, the present invention relates to a chemoenzymatic method for the preparation of a homogeneous fucosylated or nonfucosylated glycoprotein, said method comprising:
a. providing an acceptor selected from core fucosylated or nonfucosylated GlcNAc-IgG or IgG-Fc fragments; and
b. reacting the acceptor with a donor substrate in the presence a S. pyogenes Endo-S Asp-184 mutant protein or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme, wherein the donor substrate comprises a predetermined oligosaccharide component with a defined number and type of sugar residues and specific linkage types, thereby providing the homogeneous fucosylated or nonfucosylated glycoprotein.
Notably the S. pyogenes Endo-S Asp-184 mutant protein or fragment thereof can include additional mutations in the amino acid residues but importantly carries a D184 mutation.
In one embodiment, the fucosylated GlcNAc containing protein is an alpha-1-6-fucosyl-GlcNAc-protein.
In another aspect, the present invention relates to a method of IgG or IgG-Fc glycoprotein remodeling with an oligosaccharide having a predetermined oligosaccharide component with a defined number and type of sugar residues and with specific linkage types, the method comprising:
a. providing a fucosylated glycoprotein substrate comprising Fc N-glycans;
b. treating the fucosylated glycoprotein substrate with an endo-enzyme to hydrolyze the bond between the two core GlcNAc residues in the N-glycans to yield a core-fucosylated or nonfucosylated GlcNAc-IgG or IgG-Fc fragments; and
c. attaching the oligosaccharide to the Asn-linked GlcNAc moiety in the presence of an Endo-S2 mutant having an amino acid sequence selected from the group consisting of SEQ ID NO: 2 to SEQ ID NO: 20 or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme (SEQ ID NO: 1), thereby adding a predetermined the oligosaccharide component.
In a further aspect, the present invention relates to a method of fucosylated or nonfucosylated IgG or IgG-Fc fragment remodeling with an oligosaccharide having a predetermined oligosaccharide component with a defined number and type of sugar residues and with specific linkage types, the method comprising:
a. providing a fucosylated or nonfucosylated GlcNAc-IgG or IgG-Fc fragments obtained from natural or recombined sources carrying heterogeneous N-glycans;
b. treating the natural or recombinant IgG or IgG-Fc fragment with an endo-enzyme (a wild type endoglycosidase or a mutant endoglycosidase with efficient hydrolytic activity) to hydrolyze the bond between the two GlcNAc residues positioned closest to the peptide domain thereby forming a deglycosylated protein carrying the core fucosylated or nonfucosylated GlcNAc-IgG or a IgG-Fc fragment; and
c. attaching the pre-determined oligosaccharide to the GlcNAc residue to reconstitute the natural beta-1,4-glycosidic bond through transglycosylation with a S. pyogenes Endo-S2 Asp-184 mutant enzyme or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme, thereby adding a predetermined the oligosaccharide component.
Applicable oligosaccharide oxazolines include, but not limited to, high-mannose type, hybrid type, sialoglycan oxazoline and complex type N-glycan, as well as their selectively modified derivatives such as those with specific tags. Preferably, di-, tri-, tetra-, penta-, hexyl-, hepta-, octyl-, nona-, deca-, or undeca-saccharide oxazolines are utilized as donor substrates for a highly efficient chemoenzymatic synthesis of homogeneous core fucosylated or nonfucosylated IgG antibodies and IgG-Fc fragments.
In yet another aspect, the present invention relates to a method of synthesis of a modified antibody or fragment thereof, the method comprising;
a. using a naturally existing IgG antibody or a recombinant antibody or Fc domains carrying Fc N-glycans as precursors;
b. Fc deglycosylating using an endoglycosidase such as a wild Endo-S2 to deglycosylate the Fc domain to form a GlcNAc-acceptor; wherein the GlcNAc moiety is positioned on the Fc region of the antibody and the GlcNAc moiety is either core fucosylated or nonfucosylated; and
c. transglycosylating the GlcNAc moiety in the antibody with an oligosaccharide oxazoline or a sialoglycan oxazoline having a predetermined number of sugar residues under the catalysis of an enzyme selected from the group consisting of Endo-S2 mutants SEQ ID NO: 2 to SEQ ID NO: 20 or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme to form the modified antibody with the predetermined number of saccharides.
In yet another aspect, the present invention provides a method of remodeling intravenous immunoglobulins (IVIG) exhibiting Fc-sialylated glycoforms, the method comprising:
a. providing an IVIG carrying Fc N-glycans;
b. Fc deglycosylating the Fc N-glycans using an endoglycosidase including Endo-S to form a GlcNAc-acceptors; wherein the GlcNAc-acceptors are positioned on the Fc region of the IVIG and the GlcNAc-acceptors are either fucosylated or nonfucosylated; and
c. transglycosylating the GlcNAc-acceptors with sialoglycan oxazoline having a predetermined number of sugar residues under the catalysis of an enzyme selected from the group consisting of Endo-S2 mutants SEQ ID NO: 2 to SEQ ID NO: 20 or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme to form a sialylated WIG.
Another aspect of the present invention provides for an IVIG preparation containing composition comprising at least 90% of homogeneous sialylated Fc glycoforms to increase anti-inflammatory activity, wherein the sialylated Fc glycoforms are synthesized using a Streptococcus pyogenes Endo-S2 Asp-184 mutant in combination with a GlcNAc moiety positioned on the Fc region of a deglycosylated IVIG and a sialoglycan oxazoline having a predetermined number of sugar residues.
In a still further aspect, the present invention relates to a method of synthesizing homogeneous core fucosylated or nonfucosylated IgG antibodies or IgG-Fc fragments, the method comprising:
a. providing a natural or recombinant IgG antibody or IgG-Fc fragment, wherein the recombinant IgG or IgG-Fc is produced from a typical protein expression system, including but not limited to yeast, insect, plant, and any mammalian expression system;
b. removing the N-glycans by an enzyme selected from the group consisting of Endo-H, Endo-A, Endo-S, Endo S2 (WT) and/or Endo-F3 to form a core fucosylated or nonfucosylated GlcNAc-containing protein;
c. providing a sugar oxazoline or sialoglycan oxazoline with a desired oligosaccharide component comprising a defined number and type of sugar residues in the chain; and
d. enzymatically transglycosylating the fucosylated or nonfucosylated GlcNAc-containing protein with a sugar oxazoline having a desired number of sugar residues or sialoglycan oxazoline having a desired number of sugar and sialic acid residues, with an endoglycosidase selected from the group consisting of a Streptococcus pyogenes Endo-S2 Asp-184 mutant enzyme or fragment thereof that exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme, thereby forming a homogeneous core fucosylated or nonfucosylated IgG antibody or IgG-Fc fragment having an extension of desired number of sugar residues and/or sialic acid.
It is envisioned that the oligosaccharide oxazoline or sialoglycan oxazoline having a predetermined oligosaccharide component with a defined number and type of sugar residues may further comprises an additional moiety or tag including, a therapeutic agent or drug such as for treating cancer, HIV or other viruses, substances that activates receptors on the cell plasma membrane, agents that affects intracellular chemistry, agents that affects cellular physics, genes, gene analogs, RNA, RNA analogs, DNA, DNA analogs, amino acid sequences of surface receptors such as CCR5 or CD4, antigenic structure having affinity for a specific antibody; amino acid sequences of receptor ligands such as gp120, gp41 or gp160, receptor antagonists, receptor blockers, enzymes, enzyme substrates, enzyme inhibitors, enzyme modulators, therapeutic proteins, protein analogs, metabolites, metabolite analogs, oligonucleotides, oligonucleotide analogs, antigens, antigen analogs, antibodies or fragments thereof, antibody analogs, an antibody different from the modified antibody which is reactive to another receptor bacteria, viruses, inorganic ions, metal ions, metal clusters, polymers, fluorescent compounds and any combinations thereof.
As such, the present invention further provides a delivery device for delivering a drug or therapeutic agent having biological activity to treat a condition, the delivery device comprising: a remodeled IgG or IgG-Fc fragment having a predetermined sugar chain or sialoglycan and a therapeutic agent or drug attached to the terminal sugar residue or sialic acid.
The present invention envisions modifying monoclonal antibodies related to HIV including, but not limited to 17b, 48d, A32, C11, 2G12, F240, IgG1b12, 19e, X5, TNX-355 and F91, all of which are commercially available.
Further antibodies related to cancer or other diseases may also be remodeled for individual fit to certain receptors thereby increasing biological activity, the monoclonal antibodies may include, but are not limited to, cetuximab, rituximab, muromonab-CD3, abciximab, daclizumab, basiliximab, palivizumab, infliximab, trastuzumab, gemtuzumab ozogamicin, alemtuzumab, ibritumomab tiuxetan, adalimumab, omalizumab, tositumomab, I-131 tositumomab, efalizumab, bevacizumab, panitumumab, pertuzumab, natalizumab, etanercept, IGN101 (Aphton), volociximab (Biogen Idec and PDL BioPharm), Anti-CD80 mAb (Biogen Idec), Anti-CD23 mAb (Biogen Idel), CAT-3888 (Cambridge Antibody Technology), CDP-791 (Imclone), eraptuzumab (Immunomedics), MDX-010 (Medarex and BMS), MDX-060 (Medarex), MDX-070 (Medarex), matuzumab (Merck), CP-675,206 (Pfizer), CAL (Roche), SGN-30 (Seattle Genetics), zanolimumab (Serono and Genmab), adecatumumab (Sereno), oregovomab (United Therapeutics), nimotuzumab (YM Bioscience), ABT-874 (Abbott Laboratories), denosumab (Amgen), AM 108 (Amgen), AMG 714 (Amgen), fontolizumab (Biogen Idec and PDL BioPharm), daclizumab (Biogent Idec and PDL BioPharm), golimumab (Centocor and Schering-Plough), CNTO 1275 (Centocor), ocrelizumab (Genetech and Roche), HuMax-CD20 (Genmab), belimumab (HGS and GSK), epratuzumab (Immunomedics), MLN1202 (Millennium Pharmaceuticals), visilizumab (PDL BioPharm), tocilizumab (Roche), ocrerlizumab (Roche), certolizumab pegol (UCB, formerly Celltech), eculizumab (Alexion Pharmaceuticals), pexelizumab (Alexion Pharmaceuticals and Procter & Gamble), abciximab (Centocor), ranibizimumab (Genetech), mepolizumab (GSK), TNX-355 (Tanox), or MYO-029 (Wyeth).
A still further aspect of the invention relates to a method of remodeling an antibody which initially includes a heterogeneous sugar chain, the method comprising:
a. removing the heterogeneous sugar chain from the antibody with an endoglycosidase to leave a single fucosylated- or nonfucosylated-GlcNAc moiety attached to an original glycosylation site; and
b. transferring a core oligosaccharide or sialoglycan oxazoline with at least one tag to the fucosylated- or -nonfucosylated GlcNAc moiety by an endoglycosidase catalyzed transglycosylation to yield a tagged antibody, wherein the endoglycosidase is selected from the group consisting of Endo-S2 mutants SEQ ID NO: 2 to SEQ ID NO: 20 or fragment thereof that includes the catalytic domain and exhibits increased transglycosylation and reduced hydrolytic activity relative to the wild type Endo-S2 enzyme.
The tag moiety may include, but is not limited to, antigens, therapeutic drugs such as for cancer or HIV, toxins, fluorescent probes, biotin, PEG species, lipids, or nucleotides.
In yet another aspect, the present invention provides for Antibody-drug conjugates or ADCs wherein the antibody can be modified according to the present invention and are designed as a targeted therapy for the treatment of people with cancer. Specifically, an ADC contains two parts: a monoclonal antibody and a small amount of a highly potent cytotoxic drug, linked to the antibody. When the ADC's antibody binds with a particular receptor on the target cell's surface, the linkage breaks, and the ADC releases a lethal toxin into the cell. Specific monoclonal antibodies are described herein later and also possible cytotoxic drugs. Thus, the present invention provides for a modified antibody further comprising an additional moiety including, a therapeutic agent for treating cancer such as a chemokine and/or a cytokine thereby forming an Antibody-drug conjugate (ADC).
In another aspect, the present invention provides for a composition comprising at least one Streptococcus pyogenes Endo-S2 mutant selected from the group consisting of D184M (SEQ ID NO:7) and D184Q (SEQ ID No: 4).
In yet another aspect, the present invention provides a substantially homogeneous preparation of core fucosylated or nonfucosylated antibody or Fc fragment thereof having a predetermined oligosaccharide moiety, wherein the substantially homogeneous preparation is produced by any of the aforementioned methods. Also provided are compositions comprising such homogeneous preparations.
In another aspect, the present invention provides for a method of treatment using a remodeled antibody having a desired glycosylation state and/or sialylated form in an amount sufficient to modulate biological activity in the treated subject.
In a further aspect, the present invention provides for a kit including a least one Streptococcus pyogenes Endo-S2 mutant selected from the group consisting of SEQ ID NO: 2 to 20 and preferably D184M (SEQ ID NO:7), D184E (SEQ ID NO: 8) and D184Q (SEQ ID NO: 4).
Other aspects, features and embodiments of the invention will be more fully apparent from the ensuing disclosure and appended claims.
The present invention provides for novel glycosynthase EndoS2 Asp 184 mutants that show remarkable transglycosylation efficiency capable of transferring complex, high mannose, and Hybrid type N-glycans from activated glycan oxazolines to deglycosylated intact antibodies without product hydrolysis. It has been found herein that the glycosynthase EndoS2 Asp 184 mutants acted efficiently on both core-fucosylated and nonfucosylated GlcNAc-Fc domain of intact antibodies to provide various defined IgG glycoforms. As described herein the Endo-S2 did possess potent transglycosylation activity, and the systematic site-directed mutagenesis led to the discovery of several glycosynthase mutants, including D184M and D184Q, that showed remarkable transglycosylation activity without apparent product hydrolysis activity. Moreover, it is shown herein that the Endo-S2 glycosynthases demonstrated remarkably relaxed substrate specificity, being capable of transferring three major types (complex, high-mannose, and hybrid type) of N-glycans for antibody glycosylation remodeling. Further, as further described herein, it was found that the Endo-S2 glycosynthase mutants were much more active in general than the Endo-S mutants for transglycosylation. A highly efficient glycosylation remodeling of two therapeutic monoclonal antibodies, rituximab and trastuzumab (Herceptin), is described. Further, antibodies and intravenous immunoglobulins were transformed into Fc fully sialylated glycoforms having increased anti-inflammatory activity. Still further, the present invention provides for a homogeneous nonfucosylated glycoform having increased ADCC activity with enhanced FcγIIIa receptor-binding activity and azido-tagged glycoforms that can be further transformed into other glycoforms.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of immunology, molecular biology, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook, et al. MOLECULAR CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)).
It is understood that aspects of the present invention described herein include “consisting” and/or “consisting essentially of” aspects.
As used in the specification herein, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one. As used herein “another” may mean at least a second or more.
As used herein, “biological activity” refers to pharmacodynamic and pharmacokinetic properties including, for example, molecular affinity or resultant biochemical or physiological effect, receptor affinity or resultant biochemical or physiological effect, non-receptor affinity or biochemical or physiological effect, efficacy, bioavailability, absorption, distribution, metabolism, or elimination.
As used herein, “sugar” refers to an oxidized or unoxidized carbohydrate-containing molecule, including, but not limited to, a monosaccharide, disaccharide, trisaccharide, oligosaccharide, or polysaccharide, including, for example, N-acetylglucosamine, mannose, galactose, N-acetylneuraminic acid (sialic acid), glucose, fructose, fucose, sorbose, rhamnose, mannoheptulose, N-acetylgalactosamine, dihydroxyacetone, xylose, xylulose, arabinose, glyceraldehyde, sucrose, lactose, maltose, trehalose, cellobiose or any combination thereof of the L- or D-isomer. Sugar further refers to, such molecules produced naturally, recombinantly, synthetically, and/or semi-synthetically.
As used herein, “homogenous” refers to core-fucosylated glycoproteins or nonfucosylated glycoproteins wherein the oligosaccharide component comprises at least 75%, more preferably at least 90%, and most preferably at least 95% of the same number and types of sugar residues.
As used herein, “protein” or “glycoprotein” is interchangeable with the terms peptide and glycopeptide.
As used herein, “homology” refers to amino acid sequence having substantial identity or similarity between two polypeptides and having at least 85%, and more preferably at least 95% similarity to a reference polypeptide. For polypeptides, the length of comparison to obtain the above-described percent homologies between sequences will generally be at least 25 amino acids, alternatively at least 50 amino acids, more likely at least 100 amino acids, and most likely 200 amino acids or more. Substantially identity or homologous polypeptides include additions, truncations, internal deletions or insertions, conservative and non-conservative substitutions, or other modifications located at positions of the amino acid sequence which do not destroy the function of the endoglycosidase. Those of skill in the art will recognize the numerous amino acids that can be modified or substituted with other chemically similar residues without substantially altering activity.
As used herein, “modulates” refers to an increase or decrease in “biological activity”, as defined above, when comparing to a glycosylation-engineered antibody of the present invention to a non-glycosylation-engineered antibody.
As used herein, “immunoglobulin molecule” or “antibodies,” refers to molecules that contain an antigen binding site which specifically binds an antigen or an Fc region that binds to cell receptors. Structurally, the simplest naturally occurring antibody (e.g., IgG) comprises four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. The natural immunoglobulins represent a large family of molecules that include several types of molecules, such as IgD, IgG, IgA, IgM and IgE. The term also encompasses hybrid antibodies, or altered antibodies, and fragments thereof, including but not limited to Fab fragment(s) and Fc fragment(s).
Antibodies can be fragmented using conventional techniques as described herein and the fragments screened for utility in the same manner as described for whole antibodies. A Fab fragment of an immunoglobulin molecule is a multimeric protein consisting of the portion of an immunoglobulin molecule containing the immunologically active portions of an immunoglobulin heavy chain and an immunoglobulin light chain covalently coupled together and capable of specifically combining with an antigen. Fab and Fc fragments can be prepared by proteolytic digestion of substantially intact immunoglobulin molecules with papain using methods that are well known in the art. However, a Fab or Fc fragment may also be prepared by expressing in a suitable host cell the desired portions of immunoglobulin heavy chain and immunoglobulin light chain using methods known in the art.
As used herein, with respect to antibodies, “substantially pure” means separated from those contaminants that accompany it in its natural state or those contaminants generated or used in the process of the obtaining the antibody. This term further includes the desired product having a single glycosylation state, whether or not this state includes glycosylation at a single site or multiple sites. Typically, the antibody is substantially pure when it constitutes at least 60%, by weight, of the antibody in the preparation. For example, the antibody in the preparation is at least about 75%, in certain embodiments at least about 80%, in certain embodiments at about 85%, in certain embodiments at least about 90%, in certain embodiments at least about 95%, and most preferably at least about 99%, by weight, of the desired antibody. A substantially pure antibody includes a naturally, recombinantly, or synthetically produced antibody.
As used herein, “therapeutically effective amount” refers to an amount that results in an improvement or remediation of the symptoms of the disease or condition.
Antigens useful for attachment as a tag to a modified fucosylated or nonfucosylated glycoprotein of the present invention and more preferably an antibody or fragment thereof may be a foreign antigen, an endogenous antigen, fragments thereof, or variants having the same functional activity.
As used herein, “endogenous antigen” refers to a protein or part thereof that is naturally present in the recipient animal cell or tissue, such as a cellular protein, an immunoregulatory agent, or a therapeutic agent.
As used herein, “foreign antigen” refers to a protein or fragment thereof, which is foreign to the recipient animal cell or tissue including, but not limited to, a viral protein, a parasite protein, an immunoregulatory agent, or a therapeutic agent.
The foreign antigen may be a protein, an antigenic fragment or antigenic fragments thereof that originate from viral and parasitic pathogens.
Alternatively, the foreign antigen may be encoded by a synthetic gene and may be constructed using conventional recombinant DNA methods; the synthetic gene may express antigens or parts thereof that originate from viral and parasitic pathogens. These pathogens can be infectious in humans, domestic animals or wild animal hosts.
The foreign antigen can be any molecule that is expressed by any viral or parasitic pathogen prior to or during entry into, colonization of, or replication in their animal host.
The viral pathogens, from which the viral antigens are derived include, but are not limited to, Orthomyxoviruses, such as influenza virus (Taxonomy ID: 59771); Retroviruses, such as RSV, HTLV-1 (Taxonomy ID: 39015) and HTLV-II (Taxonomy ID: 11909); Herpes viruses, such as EBV (Taxonomy ID: 10295), CMV (Taxonomy ID: 10358) or herpes simplex virus (ATCC #: VR-1487); Lentiviruses, such as HIV-1 (Taxonomy ID: 12721) and HIV-2 Taxonomy ID: 11709); Rhabdoviruses, such as rabies; Picornoviruses, such as Poliovirus (Taxonomy ID: 12080); Poxviruses, such as vaccinia Taxonomy ID: 10245); Rotavirus Taxonomy ID: 10912); and Parvoviruses, such as adeno-associated virus 1 (Taxonomy ID: 85106).
Examples of viral antigens include, but are not limited to, the human immunodeficiency virus antigens Nef (National Institute of Allergy and Infectious Disease HIV Repository Cat. #183; GenBank accession #AF238278), Gag, Env (National Institute of Allergy and Infectious Disease HIV Repository Cat. #2433; GenBank accession #U39362), Tat (National Institute of Allergy and Infectious Disease HIV Repository Cat. #827; GenBank accession #M13137), Rev (National Institute of Allergy and Infectious Disease HIV Repository Cat. #2088; GenBank accession #L14572), Pol (National Institute of Allergy and Infectious Disease HIV Repository Cat. #238; GenBank accession #AJ237568) and T cell and B cell epitopes of gp120; the hepatitis B surface antigen (GenBank accession #AF043578); rotavirus antigens, such as VP4 (GenBank accession #AJ293721) and VP7 (GenBank accession #AY003871); influenza virus antigens, such as hemagglutinin (GenBank accession #AJ404627); nucleoprotein (GenBank accession #AJ289872); and herpes simplex virus antigens, such as thymidine kinase (GenBank accession #AB047378).
The bacterial pathogens, from which the bacterial antigens are derived, include but are not limited to, Mycobacterium spp., Helicobacter pylori, Salmonella spp., Shigella spp., E. coli, Rickettsia spp., Listeria spp., Legionella pneumoniae, Pseudomonas spp., Vibrio spp., and Borellia burgdorferi.
Examples of protective antigens of bacterial pathogens include the somatic antigens of enterotoxigenic E. coli, such as the CFA/I fimbrial antigen and the nontoxic B-subunit of the heat-labile toxin; pertactin of Bordetella pertussis, adenylate cyclase-hemolysin of B. pertussis, fragment C of tetanus toxin of Clostridium tetani, OspA of Borellia burgdorferi, protective paracrystalline-surface-layer proteins of Rickettsia prowazekii and Rickettsia typhi, the listeriolysin (also known as “Llo” and “Hly”) and/or the superoxide dismutase (also known as “SOD” and “p60”) of Listeria monocytogenes; the urease of Helicobacter pylori, and the receptor-binding domain of lethal toxin and/or the protective antigen of Bacillus anthrax.
Example of antigens from biological weapons or pathogens include, but are not limited to, smallpox, anthrax, tularemia, plague, listeria, brucellosis, hepatitis, vaccinia, mycobacteria, coxsackievirus, tuberculosis, malaria, erhlichosis and bacterial meningitis.
The parasitic pathogens, from which the parasitic antigens are derived, include but are not limited to, Plasmodium spp., such as Plasmodium falciparum (ATCC #: 30145); Trypanosome spp., such as Trypanosoma cruzi (ATCC #: 50797); Giardia spp., such as Giardia intestinalis (ATCC #: 30888D); Boophilus spp.; Babesia spp., such as Babesia microti (ATCC #: 30221); Entamoeba spp., such as Entamoeba histolytica (ATCC #: 30015); Eimeria spp., such as Eimeria maxima (ATCC #40357); Leishmania spp., (Taxonomy ID: 38568); Schistosome spp., such as Schistosoma mansoni (GenBank accession #AZ301495); Brugia spp., such as Brugia malayi (GenBank accession #BE352806); Fascida spp., such as Fasciola hepatica (GenBank accession #AF286903); Dirofilaria spp., such as Dirofilaria immitis (GenBank accession #AF008300); Wuchereria spp., such as Wuchereria bancrofti (GenBank accession #AF250996); and Onchocerca spp; such as Onchocerca volvulus (GenBank accession #BE588251).
Examples of parasite antigens include, but are not limited to, the pre-erythrocytic stage antigens of Plasmodium spp. such as the circumsporozoite antigen of P. falciparum (GenBank accession #M22982) P vivax (GenBank accession #M20670); the liver stage antigens of Plasmodium spp, such as the liver stage antigen 1 (as referred to as LSA-1; GenBank accession #AF086802); the merozoite stage antigens of Plasmodium spp; such as the merozoite surface antigen-1 (also referred to as MSA-1 or MSP-1; GenBank accession #AF199410); the surface antigens of Entamoeba histolytica, such as the galactose specific lectin (GenBank accession #M59850) or the serine rich Entamoeba histolytica protein; the surface proteins of Leishmania spp, such as 63 kDa glycoprotein (gp63) of Leishmania major (GenBank accession #Y00647 or the 46 kDa glycoprotein (gp46) of Leishmania major; paramyosin of Brugia malayi (GenBank accession #U77590; the triose-phosphate isomerase of Schistosoma mansoni (GenBank accession #W06781; the secreted globin-like protein of Trichostrongylus colubriformis (GenBank accession #M63263; the glutathione-S-transferases of Fasciola hepatica (GenBank accession #M77682; Schistosoma bovis (GenBank accession #M77682); S. japonicum (GenBank accession #U58012; and KLH of Schistosoma bovis and S. japonicum (Bashir, et al., supra).
Examples of tumor specific antigens include prostate specific antigen (PSA), TAG-72 and CEA; human tyrosinase (GenBank accession #M27160); tyrosinase-related protein (also referred to as TRP; GenBank accession #AJ132933); and tumor-specific peptide antigens.
Examples of transplant antigens include the CD3 molecule on T cells and histocompatibility antigens such as HLA A, HLA B, HLA C, HLA DR and HLA.
Examples of autoimmune antigens include IAS β chain, which is useful in therapeutic vaccines against autoimmune encephalomyelitis (GenBank accession #D88762); glatamic acid decarboxylase, which is useful in therapeutic vaccines against insulin-dependent type 1 diabetes (GenBank accession #NM013445); thyrotropin receptor (TSHr), which is useful in therapeutic vaccines against Grave's disease (GenBank accession #NM000369) and tyrosinase-related protein 1, which is useful in therapeutic vaccines against vitiligo (GenBank accession #NM000550).
HIV drugs that may be used in the construction of the tagged antibodies or fragments thereof include, but are not limited to antiviral agents such as nucleoside RT inhibitors, CCR5 inhibitors/antagonists, viral entry inhibitors and their functional analogs. Specifically, an antiviral agent may nucleoside RT inhibitors, such as Zidovudine (ZDV, AZT), Lamivudine (3TC), Stavudine (d4T), Didanosine (ddl), Zalcitabine (ddC), Abacavir (ABC), Emirivine (FTC), Tenofovir (TDF), Delaviradine (DLV), Efavirenz (EFV), Nevirapine (NVP), Saquinavir (SQV), Ritonavir (RTV), Indinavir (IDV), Nelfinavir (NFV), Amprenavir (APV), Lopinavir (LPV), Atazanavir, Combivir (ZDV/3TC), Kaletra (RTV/LPV), Trizivir (ZDV/3TC/ABC);
CCR5 inhibitors/antagonists, such as SCH-C, SCH-D, PRO 140, TAK 779, TAK-220, RANTES analogs, AK602, UK-427, 857, monoclonal antibodies; and viral entry inhibitors, such as Fuzeon (T-20) (enfuvirtide), NB-2, NB-64, T-649, T-1249, SCH-C, SCH-D, PRO 140, TAK 779, TAK-220, RANTES analogs, AK602, UK-427, 857; and functional analogs or equivalents thereof.
It is envisioned that many different fucosylated glycoproteins and nonfucosylated glycoproteins can be modified according to the methods of the present invention or used as a therapeutic agent for conjugation to a terminal sugar including but not limited to, adrenocorticotropic hormone (ACTH); adrenocorticotropic hormone derivatives (e.g., ebiratide); angiotensin; angiotensin II; asparaginase; atrial natriuretic peptides; atrial sodium diuretic peptides; bacitracin; beta-endorphins; blood coagulation factors VII, VIII and IX; blood thymic factor (FTS); blood thymic factor derivatives; bombesin; bone morphogenic factor (BMP); bone morphogenic protein; bradykinin; caerulein; calcitonin gene related polypeptide (CGRP); calcitonins; CCK-8; cell growth factors (e.g., EGF; TGF-alpha; TGF-beta; PDGF; acidic FGF; basic FGF); cerulein; chemokines; cholecystokinin; cholecystokinin-8; cholecystokinin-pancreozymin (CCK-PZ); colistin; colony-stimulating factors (e.g. CSF; GCSF; GMCSF; MCSF); corticotropin-releasing factor (CRF); cytokines; desmopressin; dinorphin; dipeptide; dismutase; dynorphin; eledoisin; endorphins; endothelin; endothelin-antagonistic peptides; endotherins; enkephalins; enkephalin derivatives; epidermal growth factor (EGF); erythropoietin (EPO); follicle-stimulating hormone (FSH); gallanin; gastric inhibitory polypeptide; gastrin-releasing polypeptide (GRP); gastrins; G-CSF; glucagon; glutathione peroxidase; glutathio-peroxidase; gonadotropins (e.g., human chorionic gonadotrophin and .alpha. and .beta. subunits thereof); gramicidin; gramicidines; growth factor (EGF); growth hormone-releasing factor (GRF); growth hormones; hormone releasing hormone (LHRH); human artrial natriuretic polypeptide (h-ANP); human placental lactogen; insulin; insulin-like growth factors (IGF-I; IGF-II); interferon; interferons (e.g., alpha- beta- and gamma-interferons); interleukins (e.g. 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11 and 12); intestinal polypeptide (VIP); kallikrein; kyotorphin; luliberin; luteinizing hormone (LH); luteinizing hormone-releasing hormone (LH-RH); lysozyme chloride; melanocyte-stimulating hormone (MSH); melanophore stimulating hormone; mellitin; motilin; muramyl; muramyldipeptide; nerve growth factor (NGF); nerve nutrition factors (e.g. NT-3; NT-4; CNTF; GDNF; BDNF); neuropeptide Y; neurotensin; oxytocin; pancreastatin; pancreatic polypeptide; pancreozymin; parathyroid hormone (PTH); pentagastrin; polypeptide YY; pituitary adenyl cyclase-activating polypeptides (PACAPs); platelet-derived growth factor; polymixin B; prolactin; protein synthesis stimulating polypeptide; PTH-related protein; relaxin; renin; secretin; serum thymic factor; somatomedins; somatostatins derivatives; superoxide dismutase; taftsin; tetragastrin; thrombopoietin (TPO); thymic humoral factor (THF); thymopoietin; thymosin; thymostimulin; thyroid hormone releasing hormone; thyroid-stimulating hormone (TSH); thyrotropin releasing hormone TRH); trypsin; tuftsin; tumor growth factor (TGF-alpha); tumor necrosis factor (TNF); tyrocidin; urogastrone; urokinase; vasoactive intestinal polypeptide; and vasopressin.
Fucosylated and nonfucosylated glycoproteins are important classes of biomolecules that play crucial roles in many biological events such as cell adhesion, tumor metastasis, pathogen infection, and immune response. As indicated previously herein, a major problem in structural and functional studies of fucosylated or nonfucosylated glycoproteins is their structural microheterogeneity. Natural and recombinant fucosylated or nonfucosylated glycoproteins are typically produced as a mixture of glycoforms that differ only in the structure of the pendent oligosaccharides.
The remodeled glycoproteins, such as antibodies can be subjected to any further structural modifications that are necessary or desired, including, without limitation, glycosyl transfer, and selective ligation (e.g., click chemistry, Staudinger reaction, etc.) to introduce the additional functional groups or tags. The functional groups can be of any suitable type, including, without limitation, toxins, special antigens (such as alpha-Gal), radioactive species, photoactive species, PEGs, etc. The glycoprotein can be catalytically reacted in a “click chemistry” cycloaddition reaction of the azide functionality of the glycoprotein with an alkyne bearing the functional moiety of interest. The azido and alkyne functional groups can be switched in the respective ligation components, and the glycoprotein can be functionalized with an alkynyl functionality and reacted with an azide-functionalized compound including the moiety of interest. It will also be appreciated that other ligation pairs can be devised for the click chemistry reaction.
The fucosylated and nonfucosylated glycoproteins, produced according to the methods described herein, can be used for diagnosis and therapeutics. Approximately two-thirds of therapeutic proteins used on the market and/or currently in clinical trials are glycoproteins. However, the structural heterogeneity in different glycoforms of natural and recombinant glycoproteins presents a major barrier in developing glycoprotein-based drugs, as different glycoforms may have different biological activities and controlling glycosylation to a homogeneous glycoform is extremely difficult during expression. The previous discovery of the transglycosylation activity of a class of endoglycosidases represents a major advance in the field for glycosylation engineering to enhance glycoproteins' therapeutic and diagnostic potentials and the Endo-S2 mutants of the present invention are able to transglycosylate fucosylated and nonfucosylated natural and recombinant glycoproteins without the negative aspects of hydrolysis.
The features and advantages of the present invention are more fully shown by the following non-limiting examples.
Generation of Endo-S2 Glycosynthase Mutants and their Use for Glycosylation Remodeling of Intact Monoclonal Antibody Rituximab
Glycosynthases have been previously made from several GH85 endoglycosidases (ENGases), including EndoA, EndoM, EndoD and GH18 endoglycosidase EndoS, by site-directed mutagenesis of a key asparagine (Asn) in GH85 family or aspartic acid (Asp) residue in GH18 family responsible for promoting oxazolinium ion intermediate formation during hydrolysis. [36,38] Endo-S2 is an endoglycosidase belonging to the glycoside hydrolase family 18 (GH18) [33], which is in the same GH family as EndoS, EndoF1, EndoF2, and EndoF3 that were recently shown to have transglycosylation activity. Based on the assumption that EndoS2-catalyzed hydrolysis also proceeds by a substrate-assisted mechanism involving the formation of an oxazolinium ion intermediate, as demonstrated by other GH18 endoglycosidases such as EndoS, potential glycosynthases from Endo-S2 were created by identifying and mutating the residue responsible for promoting oxazolinium ion formation. Previous structural and mutagenesis studies on Endo-S have shown that an aspartic acid residue at position 233 (D233) is responsible for promoting oxazoline formation and that the E235 residue is the general acid/base for catalytic hydrolysis [47, 48]. Sequence alignment of EndoS2 with EndoS (
Rituximab, a therapeutic monoclonal antibody, was used as a model mAb to examine the deglycosylation activity and potential transglycosylation activity of the enzymes. The major Fc glycans of commercial rituximab are core-fucosylated biantennary complex type oligosaccharides carrying 0-2 galactose moieties named G0F, G1F, and G2F glycoforms, respectively, as revealed in
The transglycosylation was further characterized by LC-MS analysis. The heavy chain and light chain of rituximab were separated under a LC-MS condition. Deconvolution of the light chain MS data gave a mass of 23 039 (
In addition to the sialylated complex type N-glycan oxazoline (2), the EndoS2 mutants were equally efficient to use the high mannose Man9GlcNAc core oxazoline (3) and the sialo hybrid type oxazoline (4) for rituximab glycoengineering, leading to the formation of the corresponding homogeneous glycoforms, (6) and (7), respectively (
Glycoengineering of Rituximab to Provide Nonfucosylated Complex, High Mannose, and Hybrid Glycoforms
For anticancer therapy, nonfucosylated IgG glycoforms are desirable as it has been previously demonstrated that mAbs with low-fucose contents of Fc N-glycans showed enhanced ADCC activity in vitro and enhanced anticancer efficacy in vivo, particularly for those patients carrying the low affinity F158 allele of the FcγIIIa receptor. [8, 39, 40, 49]. However, no α-fucosidases is available to remove the α1,6-fucose in the intact rituximab. The α-1,6-fucose moiety might be shielded by the Fc domain and/or the complex N-glycan, making it inaccessible to α-fucosidases. It was theorized that, upon deglycosylation, the resulting Fuc(α1,6)GlcNAc glycoform of rituximab might be more accessible to α-fucosidases. Indeed, after deglycosylation with EndoS2, most of the α-1,6-fucose moiety could be removed by overnight incubation with α1,6-fucosidase from Lactobacillus casei to give the GlcNAc-containing rituximab (8). The result is confirmed with LC-MS (
Comparison of the Transglycosylation Activity of Different Mutants of EndoS2 D184
The activities of EndoS2-D184A, D184N, and D184Q were compared of transferring sialo bianntenary complex glycan oxazoline (2) to fucosylated GlcNAc-rituximab (1). With the same reactive conditions, the asparagine (N) mutant transferred more than 30% of oxazoline to the acceptor in five minutes while the alanine (A) and glutamine (Q) mutants transfer less than 20% (
Cloning, Expression and Characterization of Endo-S2
cDNA sequence encoding Endo-S2 (44-843 of SEQ ID NO: 1) (The Genbank accession number for the Endo-S2 gene (ndoS2) is ACI61688) was cloned into a pET22b-CPD vector, which adds to the C-terminus of the expressed protein the cysteine protease domain (CPD) of the Vibrio cholerae MARTX toxin and a 10× histidine tag [35] (SEQ ID NO 22). It was recently reported that a high level, soluble expression of Endo-F3 and its mutants could be achieved using this vector [32]. In the alternative, the cDNA sequence for encoding Endo-S2 may include (1, and 44-843 amino acids of SEQ ID NO: 1). Following a similar method, the Endo-S2 was successfully expressed in E. coli and was readily purified using immobilized metal ion affinity chromatography (IMAC) to obtain the soluble enzyme with a yield of more than 20 mg/L. The recombinant Endo-S2 showed high hydrolysis activity as demonstrated by its rapid deglycosylation of commercial rituximab, which was monitored by LC-MS analysis.
Generation of Glycosynthase Mutants from Endo-S2
Glycosynthase mutants from endoglycosidases of both GH85 and GH18 family were generated by site-directed mutation at a key residue that is responsible for promoting the formation of the oxazolinium ion intermediate during hydrolysis, which proceeds in a substrate-assisted mechanism. These include a key asparagine residue for endoglycosidases Endo-A (Asn171) [36], Endo-M (Asn175) [37,38], and Endo-D (Asn322) [24] of the GH85 family, or a key aspartic acid residue for the GH18 family endoglycosidases Endo-S (Asp233) [25] and Endo-F3 (Asp-165) [32]. Sequence alignment of Endo-S2 and Endo-S revealed that the Asp-184 of Endo-S2 was the residue equivalent to the Asp233 of Endo-S essential for promoting oxazolinium ion formation in hydrolysis (
Notably, it is envisioned that unnatural proteins may also be used in the substitution. Examples of unnatural amino acids that can be used by the translation system include: an unnatural analogue of a tyrosine amino acid; an unnatural analogue of a glutamine amino acid; an unnatural analogue of a phenylalanine amino acid; an unnatural analogue of a serine amino acid; an unnatural analogue of a threonine amino acid; an alkyl, aryl, acyl, azido, cyano, halo, hydrazine, hydrazide, hydroxyl, alkenyl, alkynl, ether, thiol, sulfonyl, seleno, ester, thioacid, borate, boronate, phospho, phosphono, phosphine, heterocyclic, enone, imine, aldehyde, hydroxylamine, keto, or amino substituted amino acid, or any combination thereof.
Comparative Study on the Hydrolysis and Transglycosylation Activity of 19 Mutants and WT
The hydrolysis activities on Fc N-glycans in an intact antibody and the transglycosylation activities with glycan oxazoline were assessed by following the scheme as shown in
Endo-S2 Glycosynthases Show Remarkably Broad Substrate Specificity in Transglycosylation
Rituximab, a therapeutic monoclonal antibody, was used as a model to examine the transglycosylation activity of the Endo-S2 D184 mutants. The major Fc glycans of commercial rituximab are core-fucosylated bi-antennary complex type oligosaccharides carrying 0-2 galactose moieties named G0F, G1F, and G2F glycoforms, respectively. The general glycosylation remodeling approach was presented in
In addition to the complex-type N-glycan, the specificity of Endo-S2 was further tested with high-mannose-type (HM) Man9GlcNAc oxazoline (7) and sialo hybrid-type (Hyb) Neu5AcGalGlcNAcMan5GlcNAc oxazoline (5) as donor substrate in the transglycosylation reactions. The reactions led to the formation of the corresponding homogeneous glycoforms, (8) and (6), respectively (
Endo-S2 Based Glycosylation Remodeling for Making Nonfucosylated Glycoforms
For anticancer therapy, nonfucosylated IgG glycoforms are desirable as it has been previously demonstrated that mAbs with low-fucose contents of Fc glycosylation showed enhanced ADCC activity in vitro and enhanced anticancer efficacy in vivo, particularly for those patients carrying the low affinity F158 allele of the FcγIIIa receptor [8, 9, 39, 40]. To test whether Endo-S2 can glycosylate non-fucosylated IgG, Fucα1,6GlcNAc-rituximab (2) was incubated with a recombinant α1,6-fucosidase from Lactobacillus casei [41] to give GlcNAc-rituximab (9) lacking the core-fucose. Endo-S2 D184M catalyzed transglycosylation of GlcNAc-rituximab (9) was carried out with a sialo biantennary complex-type (CT) N-glycan oxazoline (10). It was found that the D184M mutant could efficiently transfer the N-glycan to the GlcNAc acceptor in the antibody to give the fully galactosylated and nonfucosylated glycoform (11) in an essentially quantitative conversion. The deconvoluted ESI-MS of the heavy chain of transglycosylation product (11) showed a single species at 50684, as shown in
Comparison of Transglycosylation Efficiency on Different N-Glycan Substrates by Endo-S2 D184M Mutant
To further characterize the N-glycan substrate preference of Endo-S2 D184M, three parallel transglycosylation reactions were carried out with the N-glycan oxazolines of the complex (SCT) type, high-mannose (HM) type, and hybrid (Hyb) type, respectively. The reaction progresses were monitored by LC-MS analysis of reaction aliquots taken at multiple time-points and the results were summarized in
Comparison of the Transglycosylation Efficiency of Typical Endo-S2 and Endo-S Mutants
Endo-S glycosynthase mutants D233Q and D233A were previously generated that transglycosylate rituximab efficiently with complex-type N-glycan oxazoline [25]. The EndoS D233 mutants have been recently used to generate homogeneous monoclonal antibodies for structural and functional studies [26-31]. To compare the transglycosylation efficiency of the glycosynthase mutants from Endo-S2 and Endo-S, the Endo-S D233Q mutant was selected, the equivalent Endo-S2 D184Q mutant and the Endo-S2 D184M mutant to catalyze three parallel transglycosylation reactions. The time-course of the transglycosylation reactions was monitored by LC-MS analysis and was summarized in
Glycosylation Remodeling of Trastuzumab (Herceptin) Using a Pair of Endo-S2 Enzymes
To demonstrate that the observed enzymatic properties of Endo-S2 and its mutants are generally applicable to antibody glycosylation remodeling, glycosylation remodeling of another monoclonal antibody was performed, trastuzumab (Herceptin), which is widely used for treatment of breast cancer. The glycosylation remodeling was assessed by the synthesis of a sialylated glycoform of trastuzumab (
To confirm that the N-glycan was attached specifically to the Asn-297 N-glycosylation site of the Fc domain, instead of other sites of the polypeptide backbone that might occur by nonenzymatic reactions as implicated in a recent publication [30], the transglycosylation product (13) was treated with PNGase F and examined the protein portion by mass spec analysis. PNGase F was highly specific and could release the Nglycans only when they were attached to the Asn side chain in an N-glycosylamide linkage at the conserved glycosylation site in N-glycoproteins. LC-MS analysis of the heavy chain of the PNGase F treated transglycosylation product (13) gave a single species of 49150 (deconvolution data), which corresponds to the polypeptide backbone of the heavy chain without any additional modifications (
Described herein is the discovery of a new class of glycosynthases derived from an endoglycosidase (Endo-S2) of the Streptococcus pyogenes M49 serotype, which showed broader substrate specificity and much more potent transglycosylation activity for antibody glycosylation remodeling than the previously reported glycosynthases, such as those derived from Endo-A, Endo-M, Endo-S, and Endo-F3. These findings were enabled by a systematic mutagenesis at the critical residue D184, coupled with comparative analysis of the hydrolysis and transglycosylation activities of the resulting 19 mutants. The experimental data also revealed remarkable difference in both the hydrolysis and transglycosylation activities among the 19 mutants (Tables 1 and 2), which would be difficult to predict without this comparative study. Several notable mutants, including the D184M and D184Q mutants, were identified that showed high transglycosylation activity for glycosylation remodeling but retained only marginal hydrolysis activity.
Comparison of the hydrolysis and transglycosylation activities of the mutants reveals several interesting features. First, most of the mutants that showed high transglycosylation activity, including the D184C, D184G, D184E, D184Y, D184 S, and D184A mutants, also possessed relatively high residual hydrolysis activity. An exception is the D184M mutant, which demonstrated remarkable transglycosylation activity but retained only residual hydrolysis activity, making it the most efficient glycosynthase for glycosylation remodeling. Secondly, most the mutants with the D184 residue being replaced by amino acids with positively charged side chains (K, R, H) or bulky hydrophobic side chains (I, L, F, W) showed very low activities in both transglycosylation and hydrolysis. But, interestingly, the D184Y mutant retained the highest hydrolytic activity among all the mutants and also possessed a relatively high transglycosylation activity.
Another important discovery is the findings of the much broader substrate specificity of the Endo-S2 derived glycosynthase mutants than that of the previously reported glycosynthases. It was found that the D184M and D184Q mutants, two notable Endo-S2 glycosynthases identified, were able to efficiently transfer all three major types of N-glycans including high-mannose type, complex type, and hybrid type, in antibody glycosylation remodeling. In addition, the Endo-S2 glycosynthases could recognize both core-fucosylated GlcNAc or nonfucosylated GlcNAc moiety at the Fc domain as an acceptor for transglycosylation. These findings significantly expand the scope of the glycosylation remodeling strategy. For example, the previously reported Endo-S and Endo-F3 are specific for complex type N-glycans and are unable to efficiently transfer high-mannose and hybrid type N-glycans, and the Endo-F3 is efficient only for core-fucosylated GlcNAc acceptor [32]. A direct comparison of the transglycosylation activity of the typical Endo-S2 and Endo-S glycosynthase mutants reveals that the Endo-S2 mutants are generally much more active than the corresponding Endo-S mutant. By an estimate of the initial rate, the D184Q mutant of Endo-S2 was at least 10-fold more active than the corresponding D233Q mutant of Endo-S, and the best Endo-S2 mutant, D184M, was estimated to be 100-fold better than the Endo-S D233Q mutant in glycosylating the deglycosylated rituximab (
Experimental Procedures
Materials—Monoclonal antibodies rituximab and trastuzumab (Herceptin) were products from Genentech Inc., (South San Francisco, Calif.). A sialo and sialoglycan complex type oxazoline was synthesized following the previously reported procedure [42]. The high mannose-type (HM) glycan (Man9GlcNAc) was prepared from soy bean flour by the previously described procedure [43]. The synthesis of hybrid type (Hyb) glycan (Neu5AcGalGlcNAcMan5GlcNAc) was achieved by a sequential enzymatic glycosylation of the Man5GlcNAc [43] under the catalysis of a β-1,2-GlcNAc transferase (GnT1) [44], a β-1,4-galactosyltransferase [45] and an α-2,6-Sialyltransferase [46]. The HM and Hybrid glycan oxazolines were synthesized following the previously described one-pot transformation procedure [42]. Endo-S D233Q from Streptococcus pyogenes was overexpressed and purified following our previous procedure [25].
Site-Directed Mutagenesis and Expression and Purification of Recombinant Endo-S2
cDNA encoding amino acids 44-843 of Endo-S2 from Streptococcus pyogenes NZ131 (serotype M49) was amplified by PCR and cloned into the pCPDLasso vector (a pET22b-CPD derivative) (35), wherein the sequence for the CPD (cysteine protease domain of the Vibrio cholerae MARTX toxin and histidine tag is set forth in SEQ ID NO: 22. For saturation mutagenesis of Asp-184 residue, a forward primer, 5′-CGTAAATTCGTGCTCAATNNNAATATCTAGTCCATCGACACCACGATCAGTT-3′, (SEQ ID NO: 23) and a reverse primer, 5′-AACTGATCGTGGTGTCGATGGACTAGATATTNNNATTGAGCACGAATTTACG-3′ (SEQ ID NO: 24), were used. Mutations were confirmed by DNA sequencing. The plasmids containing mutated Endo-S2 genes were transformed into E. coli BL21 (DE3). For simultaneous production of 20 Endo-S2 D184 variants, the transformants were cultured in 20 mL 2×YT broth media supplemented with 100 μg/mL carbenicillin. Cultures were grown at 37° C. until the cells reached an OD600 of 0.8-1.0. Then 0.5 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) was added to the culture to induce protein overproduction at 20° C. After 24 h the cells were harvested by centrifugation. The cell pellets were lysed by Bacterial Cell Lysis Buffer (Gold Biotechnology, Inc.) following manufacturer's instructions. 10× histidine (His10)-tagged EndoS2/CPD fusion proteins were purified with NiNTA Spin Columns (Qiagen). The purified EndoS2 proteins were desalted into PBS (pH 7.4) using centrifugal diafiltration with Amicon ultra filtration (10 kDa, Millipore). The protein purity was confirmed by SDS-PAGE and the concentration was measured on a NanoDrop 2000c using absorbance at 280 nm. For large-scale purification of selected Endo-S2 variants, 1 L culture is used. The cell lysate was applied to a HisTrap HP column (GE) and washed with PBS with 0.5 M NaCl and 20 mM imidazole (pH 7.4). Bound His-tagged protein was eluted with a gradient of 0-250 mM imidazole in PBS buffer. Eluted fractions containing Endo-S2 protein were pooled, concentrated and further purified by size exclusion chromatography through a HiPrep 16/60 Sephacryl S-200 HR column (GE).
Liquid Chromatography Mass Spectrometry (LC-ESI-MS) of IgG
The LC-MS analysis was performed on an Exactive Plus Orbitrap (Thermo Scientific). For intact antibody, the analysis was performed with a Waters XBridge™ BEH300 C4 column (3.5 2.1×50 mm) with a linear gradient of 5-90% MeCN containing 0.1% formic acid within 9 min at a flow rate of 0.4 ml/min. For analysis of antibody light chain and heavy chain, the IgG antibody were treated with 50 mM TCEP and heated at 37° C. for 20 min then subjected to LC-MS analysis with an Agilent Poroshell 300SB-C8 column (5 μm, 75×1 mm). The analysis was performed at 60° C. eluting with a linear gradient of 25-35% MeCN containing 0.1% formic acid within 6 min at a flow rate of 0.40 mL/min. The LC-MS analysis of PNGase F treated antibody glycoforms was performed in the same manner but included a 3-hr incubation with PNGaese F prior to TCEP treatment. Raw data was deconvoluted using MagTran (Amgen).
Deglycosylation of Rituximab by WildType Endo-S2 to Give (Fucα1,6)GlcNAc-Rituximab
Commercial rituximab in its original buffer was incubated with wild-type Endo-S2 for one hour at 37° C. with an antibody-to-enzyme ratio of 500:1 (by weight). LC-MS analyses indicated the complete cleavage of the N-glycans on the heavy chain. The deglycosylated rituximab was purified by protein A chromatography. LC-MS: calculated for the heavy chain of (Fucα1,6)GlcNAc-rituximab (2), M=49420 Da; found (m/z), 49412 (deconvolution data).
Defucosylation of (Fucα1,6)GlcNAc-Rituximab by Bacterial α-Fucosidase
A solution of (Fucα1,6)GlcNAc-rituximab (2) in a Tris-HCl buffer (50 mM, pH 7.4) was incubated with the α-fucosidase AlfC from Lactobacillus casei at 37° C., with an antibody-to-enzyme ratio of 50:1. After 16 h incubation, LC-MS monitoring indicated the complete defucosylation of (Fucα1,6)GlcNAc rituximab (2) to give the product, GlcNAc-rituximab (9). The defucosylated rituximab was purified by protein A chromatography. LC-MS: calculated for the heavy chain of GlcNAc-rituximab (9) carrying a GlcNAc moiety, M=49274 Da; found (m/z), 49265 (deconvolution data).
Enzyme Assay
Assay for the hydrolysis activity of each Endo-S2 variant (0.1 μg) was performed at 30° C. with pure sialo-complex-type (S2G2F) rituximab 3 (10 μg, 7.0 μM) as substrate in PBS buffer (pH 7.4, 10 μl). An aliquot of each reaction mixture was diluted in 0.1% formic acid to stop the reaction and analyzed by LC-MS. Relative amount of the substrate and the hydrolysis products were quantified after deconvolution of the raw data and integration of the corresponding MS peaks using MagTran. The transglycosylation reaction with synthetic sugar oxazoline was assayed as follows: (Fucα1,6)GlcNAc-rituximab (100 μg, 69 μM), SCTox (1.38 mM, 20 equivalents) was incubated with 0.1 μg of each Endo-S2 variants at 30° C. in PBS (pH 7.4, 10 μl). The reactions were stopped and analyzed as in the hydrolysis assay stated above. Experiment of each mutant was repeated at least twice to ensure the consistency of the results.
Transglycosylation of Fuc1,6 GlcNAc Rituximab with SCT-Ox, Hyb-Ox and HM-Ox by Endo-S2 D184M: Synthesis of 3, 6, 8
A solution of Fuc1,6GlcNAc-Rituximab (1 mg, 69 μM) (2) and SCTox (1.38 mM, 20 eq) (4) was incubated with Endo-S2 D184M (5 μg) at 30° C. in 100 μl of 100 mM Tris Buffer (pH 7.4) for 15 min. LC-MS analysis indicated the completion of the transglycosylation reaction. The product (3) was purified using protein A chromatography. LC-MS: calculated for the heavy chain of (3) carrying the fully sialylated bi-antennary N-glycan, M=51421 Da; found (m/z), 51412 (deconvolution data).
A solution of Fuc1,6GlcNAc-Rituximab (1 mg, 69 μM) (2) and Hybox (1.38 mM, 20 eq) (5) was incubated with Endo-S2 D184M (5 μg) at 30° C. in 100 μl of 100 mM Tris Buffer (pH 7.4) for 30 min. Then another 10 eq of Hybox (5) was added and the reaction was monitored by LC-MS of aliquots. When LC-MS analysis indicated the near completion of the transglycosylation reaction, the product (6) was purified using protein A chromatography. LC-MS: calculated for the heavy chain of (5) carrying the sialylated hybrid-type Nglycan, M=51090 Da; found (m/z), 51082 (deconvolution data).
A solution of Fuc1,6GlcNAc-Rituximab (1 mg, 69 μM) (2) and HMox (1.38 mM, 20 eq) (7) was incubated with Endo-S2 D184M (5 μg) at 30° C. in 100 μl of 100 mM Tris Buffer (pH 7.4) for 30 min. Then another 10 eq of HMox (7) was added and the reaction was monitored by LC-MS of aliquots. When LC-MS analysis indicated the completion of the transglycosylation reaction, the product (8) was purified using protein A chromatography. LC-MS: calculated for the heavy chain of (12) carrying the high-mannose-type (Man9GlcNAc2) N-glycan, M=51081 Da; found (m/z), 51074 (deconvolution data).
Transglycosylation of GlcNAc-Rituximab with CT-Ox by Endo-S2 D184M: Synthesis of 11
A solution of GlcNAc-Rituximab (1 mg, 69 μM) (9) and CTox (1.38 mM, 20 eq) (10) was incubated with Endo-S2 D184M (5 μg) at 30° C. in 100 μl of 100 mM Tris Buffer (pH 7.4) for 30 min. LC-MS analysis indicated the completion of the transglycosylation reaction. The product (11) was purified using protein A chromatography. LC-MS: calculated for the heavy chain of (11) carrying the bi-antennary N-glycan, M=50693 Da; found (m/z), 50684 (deconvolution data).
Comparison of Transglycosylation Activity of Endo-S2 D184M Mutant Using SCT-, HM- and Hyb-Oxazoline as Donor Substrates
In three separate reactions, Fuc1,6GlcNAc-Rituximab (0.2 mg, 69 μM) (2) together with SCTox (4), Hyb-ox (5) or HM-ox (7) (1.38 mM, 20 eq) was incubated with Endo-S2 D184M (1 μg) at 30° C. in 20 μl of 100 mM Tris Buffer (pH 7.4). An aliquot of reaction (0.5 μl) was taken out at several time points and dilute in 0.1% formic acid to stop the reaction. All aliquots were analyzed by LC-MS and % transglycosylation was calculated from the deconvoluted data.
Comparison of Transglycosylation Activity of Endo-S2 D184M, D184Q Mutants and Endo-S D233Q Mutant Using SCT-Oxazoline as the Donor Substrate
In three separate reactions, Fuc1,6GlcNAc-Rituximab (0.2 mg, 69 μM) (2) and SCTox (4) (1.38 mM, 20 eq) was incubated with Endo-S2 D184M, Endo-S2 D184Q or Endo-S D233Q (1 μg) at 30° C. in 20 μl of 100 mM Tris Buffer (pH 7.4). An aliquot of reaction (0.5 μl) was taken out at several time points and dilute in 0.1% formic acid to stop the reaction. All aliquots were analyzed by LC-MS and % transglycosylation was calculated from the deconvoluted data.
Transglycosylation of Fuc1,6GlcNActrastuzumab with SCT-Ox by Endo-S2 D184M
Commercial trastuzumab (lyophilized powder) was dissolved in water and deglycosylated with wildtype Endo-S2 following the same method for rituximab. For transglycosylation, a solution of Fuc1,6GlcNAc-trastuzumab (12) (1 mg, 69 μM) and SCTox (4) (1.38 mM, 20 eq) was incubated with Endo-S2 D184M (5 μg) at 30° C. in 100 μl of 100 mM Tris Buffer (pH 7.4) for 15 min. LC-MS analysis indicated the completion of the transglycosylation reaction. The product (13) was purified using protein A chromatography.
The contents of all references cited herein are hereby incorporated by reference herein for all purposes.
The present application is a continuation application of co-pending U.S. patent application Ser. No. 16/069,216, filed on Jul. 11, 2018 and now U.S. patent Ser. No. 11,008,601, which in turn claims priority of International Patent Application No. PCT/US2017/013734 filed on Jan. 17, 2017 and further claims priority to U.S. Provisional Patent Application No. 62/279,087 filed on Jan. 15, 2016, the contents of which is hereby incorporated by reference herein for all purposes.
This invention was made with government support under R01 GM096973 and R01 GM080374 awarded by the National Institutes of Health. The government has certain rights in the invention.
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| 20210269841 A1 | Sep 2021 | US |
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| 62279087 | Jan 2016 | US |
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| Parent | 16069216 | US | |
| Child | 17320703 | US |
