Patent Application
20240336946
The present invention relates to a solid-phase glycan remodeling (SPGR) system for the glycoengineering of glycoproteins to provide glycoprotein compositions comprising particular predominant glycoforms.
Protein glycosylation is a key determinant of the physical and biochemical properties of proteins in eukaryotic systems (Varki et al. in Essentials of Glycobiology, Cold Spring Harbor Laboratory Press, The Consortium of Glycobiology Editors, La Jolla, C A 2015); Spiro, Glycobiology 12, 43R-56R, doi:10.1093/glycob/12.4.43R (2002); Varki, A. in Glycobiology Vol. 27 3-49 (2017)). According to glycoproteomic analyses, over 1% of the human genome encodes glycosylation-related enzymes and more than 50% of human proteins are glycosylated (Apweiler et al., Biochim. Biophys. Acta 1473, 4-8, doi:10.1016/s0304-4165(99)00165-8 (1999)). Glycoproteins carry structurally diverse oligosaccharides, called glycans, that are involved at the interface of protein-biomolecular interactions and thus determine protein stability, selectivity, and activity. The significance of protein glycosylation to biological systems has been exemplified by several diseases associated with various cancers and the immune system (Reily et al., Nature Reviews Nephrology 15, 346-366, doi:10.1038/s41581-019-0129-4 (2019); Maverakis et al., J. Autoimmun. 57, 1-13, doi:10.1016/j.jaut.2014.12.002 (2015); Reiding et al., Front Med (Lausanne) 4, doi:10.3389/fmed.2017.00241 (2017); van de Bovenkamp et al., Journal of Immunology 196, 1435-1441, doi:10.4049/jimmunol.1502136 (2016); Munkley, Oncol. Lett. 17, 2569-2575, doi:10.3892/ol.2019.9885 (2019); Pinho & Reis, Nat. Rev. Cancer 15, 540-555, doi:10.1038/nrc3982 (2015); Schultz et al. Cancer Res. 76, 3978-3988, doi:10.1158/0008-5472.can-15-2834 (2016); Nairn et al., J. Biol. Chem. 287, 37835-37856, doi:10.1074/jbc.M112.405233 (2012)). For example, patients with rheumatoid arthritis were found to have an increased galactosylation level in their serum immunoglobulin G (IgG), though the mechanism remains elusive (Reiding et al., Front Med (Lausanne) 4, doi:10.3389/fmed.2017.00241 (2017)). Unsurprisingly, it follows that insights into the structure and function of glycans have yielded a profound impact on the development of therapeutic glycoproteins (Mimura et al., Protein Cell 9, 47-62, doi:10.1007/s13238-017-0433-3 (2018)). Manipulating glycan structures presents an effective strategy to improve their efficacy and safety by modulating immunological responses, circulatory half-life, and effector functions (Goetze et al., Glycobiology 21, 949-959, doi:10.1093/glycob/cwr027 (2011); Higel et al., Eur. J. Pharma. Biopharma. 100, 94-100, doi:https://doi.org/10.1016/j.ejpb.2016.01.005 (2016); Chiang et al., Curr. Opin. Struct. Biol. 40, 104-111, doi:10.1016/j.sbi.2016.08.008 (2016)). Thus, glycoengineering represents a versatile tool and a great opportunity to create better medicines through glycan remodeling. To achieve this goal, technologies that confer control of protein glycosylation profiles are essential.
To date, however, tools to access the diverse array of glycan structures displayed in nature remain scarce, and methods that produce a high yield of the desired glycoforms have proven to be a still greater challenge to develop despite decades of study (Wong, J. Organic Chemistry 70, 4219-4225, doi:10.1021/jo050278f (2005); Zhang et al. Drug Discovery Today 21, 740-765, doi:https://doi.org/10.1016/j.drudis.2016.01.006 (2016)). Through traditional synthetic approaches, several common glycoforms have been accessed (Fairbanks, Beilstein J. Organic Chemistry 14, 416-429, doi:10.3762/bjoc.14.30 (2018); Nagasaki et al., J. Organic Chemistry 81, 10600-10616, doi:10.1021/acs.joc.6b02106 (2016); Tang et al., J. Organic Chemistry 80, 10482-10489, doi:10.1021/acs.joc.5b01428 (2015)). These structurally-defined glycans can be installed onto glycoproteins through endoglycosidase and glycosynthase activities (Heidecke et al., Chembiochem 9, 2045-2051, doi:10.1002/cbic.200800214 (2008); Umekawa et al., J. Biol. Chem. 285, 511-521, doi:10.1074/jbc.M109.059832 (2010); Lin et al., Proc Natl Acad Sci USA 112, 10611-10616, doi:10.1073/pnas.1513456112 (2015)). While this approach has advanced our ability to control protein glycosylation, the preparation of synthetic glycans becomes increasingly difficult as the number of saccharide units increases. As a result, the installation of synthetic glycans is not practical for many applications. On the other hand, genetic engineering has been applied for controlled glycan biosynthesis by either knocking out or introducing certain glycosylation enzymes in the host cells (Malphettes et al., Biotechnol. Bioeng. 106, 774-783, doi:10.1002/bit.22751 (2010); Yang et al. Nat. Biotechnol. 33, 842-844, doi:10.1038/nbt.3280 (2015)). This strategy enables in vivo glycan remodeling and has been demonstrated to produce humanized glycoproteins in non-human cell lines (Liu et al., Proc Natl Acad Sci USA 115, 720-725, doi:10.1073/pnas.1718172115 (2018)). However, the optimization of this strategy has been impeded by the complexity of engineering glycosylation pathways. Also, micro-heterogeneity is often generated during in vivo glycan formation, which, although it is comparable to the natural phenomenon, does not provide exquisite control over the molecular structure (Higel et al., Eur. J. Pharma. Biopharma. 100, 94-100, doi:https://doi.org/10.1016/j.ejpb.2016.01.005 (2016); Kolarich et al., Nature Protocols 7, 1285-1298, doi:10.1038/nprot.2012.062 (2012)).
In recent decades, our understanding of the in vitro activity of glycosylation enzymes is growing rapidly (Peng et al., Chembiochem: a European journal of chemical biology 18, 2306-2311, doi:10.1002/cbic.201700292 (2017); Lairson et al., Annual Rev. Biochemistry 77, 521-555, doi:10.1146/annurev.biochem.76.061005.092322 (2008); Sjögren et al., Glycobiology 30, 254-267, doi:10.1093/glycob/cwz085 (2019)). Some of the enzymes can even function on intact glycoproteins, which opens a new window for glycan remodeling (Hamilton et al., Scientific Reports 7, 15907, doi:10.1038/s41598-017-15891-8 (2017); Huang et al., J. Am. Chem. Soc. 134, 12308-12318, doi:10.1021/ja3051266 (2012); Rich & Withers, Nat. Chem. Biol. 5, 206-215, doi:10.1038/nchembio.148 (2009); Ochiai et al., J. Am. Chem. Soc. 130, 13790-13803, doi:10.1021/ja805044x (2008); McArthur et al., Biochem.Society Transactions 44, 129-142, doi:10.1042/bst20150200 (2016); Tang et al., Organic & Biomolec. Chem. 14, 9501-9518, doi:10.1039/C60B01751G (2016); Li, T. et al. Nature Chemistry 11, 229-236, doi:10.1038/s41557-019-0219-8 (2019); Barb, & Prestegard, Nat Chem Biol 7, 147-153, doi:10.1038/nchembio.511 (2011)).
To further leverage the use of these enzymes, three primary challenges need to be addressed. First, most of the enzymes applied to glycan engineering have been studied based on the use of synthetic oligosaccharides and/or denatured glycoproteins as substrates. Whether or not a suite of enzymes can remodel glycosylation on intact glycoproteins is a question that persists. Second, preserving the integrity and functions of the substrates after the enzymatic reactions is advantageous, especially for therapeutic glycoproteins. Protocols with high biocompatibility are thus required. Third, to construct complex glycan structures, successive reactions using different enzymes are needed. These enzymes might require very different working conditions, such as pH and temperature. Therefore, one would need to repeat the buffer swapping and product purification processes between the enzymatic reactions, which is highly labor-intensive and time-consuming. Together, to address these issues, novel platforms that enable efficient, successive enzymatic glycan remodeling with high biocompatibility to the substrates are in great demand.
The present invention provides a solid-phase glycan remodeling (SPGR) system wherein glycosylation enzymatic reactions are carried out on glycoprotein substrates immobilized on resins. The SPGR system of the present invention enables efficient reaction swapping, substrate purification, and the recovery of both products and engineering enzymes. The present invention is particularly useful for glycoengineering immunoglobulins (e.g., antibodies or IgG) to provide antibodies that have predominantly particular glycoform profiles. The SPGR system of the present invention enables harmonization of antibody glycans into one or more of ten different glycoforms, including non-canonical structures, in 48 hours with an average conversion ratio greater than 95%. Physical and biochemical analyses indicate that the SPGR-engineered antibodies preserved integrity and functionality, suggesting that the SPGR system of the present invention has high biocompatibility to the substrates.
The present invention provides a method for remodeling the N-glycans of a composition of N-glycosylated glycoproteins, the steps comprising: (a) providing an aqueous composition of N-glycosylated glycoproteins; (b) immobilizing the N-glycosylated glycoproteins on a solid support; (c) reacting the immobilized N-glycosylated glycoproteins with a glycosylation enzyme or sequentially with two or more glycosylation enzymes to produce immobilized N-glycosylated glycoproteins comprising remodeled N-glycans; (d) eluting the N-glycosylated glycoproteins comprising the remodeled N-glycans from the solid support to provide a composition of the N-glycosylated glycoproteins comprising remodeled N-glycans.
In a further embodiment, the solid support comprises irreversibly affixed thereon a multiplicity of capture moieties that specifically bind the N-glycosylated glycoprotein.
In a further embodiment, the N-glycosylated glycoprotein comprises an antibody or antigen-binding fragment.
In a further embodiment, the multiplicity of capture moieties comprises protein A and the N-glycosylated glycoprotein comprises an antibody.
In a further embodiment, the one or more glycosylation enzymes are selected from the group consisting of exoglycosidases, endoglycosidases, and glycosyltransferases.
In a further embodiment, the exoglycosidases are selected from the group consisting of neuraminidases, galactosidases, fucosidases, and N-acetyl-glucosaminidases; and, the glycosyltransferases are selected from the group consisting of N-acetylglucosaminidyltransferases (GnTs), galactosyltransferases (GalTs), fucosyltransferases (FuTs), and sialyltransferases (SiaTs).
In a further embodiment, the endoglycosidases are selected from the group consisting of endoglycosylase A, D, F2, F3, M, and S.
In a further embodiment, the SiaTs are selected from the group consisting of a2-6 SiaT and α2-3 SiaT: the GalTs comprise β1-4GalT: the FuTs comprise α1-6 FuT; and, the GnTs are selected from the group consisting of GnTI, GnTII, GnTIII, GnTIV, and GnTV.
In a further embodiment, the immobilized N-glycosylated glycoproteins are reacted with an exoglycosidase or sequentially with two or more exoglycosidases to produce first immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof comprise two terminal mannose residues at the non-reducing end of the N-glycan, one terminal mannose linked to a central mannose residue in an α1-3 linkage and the other terminal mannose linked to the same central mannose in an α1-6 linkage, and the central mannose is linked to a chitobiose core in a 1-4 linkage wherein the GlcNAc residue at the reducing end of the chitobiose core is linked to an asparagine residue of an N-glycosylation site in the N-glycosylated glycoprotein.
In a further embodiment, the first immobilized N-glycosylated glycoproteins are reacted with a GnTI in the presence of UDP-GlcNAc to produce second immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the second immobilized N-glycosylated glycoproteins are reacted with a GalT in the presence of UDP-galactose to produce third immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the third immobilized N-glycosylated glycoproteins are reacted with a SiaT in the presence of CMP-sialic acid to produce fourth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a sialic acid residue linked to the non-reducing end of the galactose residue linked to the non-reducing end of the GlcNAc residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the second immobilized N-glycosylated glycoproteins are reacted with a GnTII in the presence of UDP-GlcNAc to produce third immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third immobilized N-glycosylated glycoproteins are reacted with a GalT in the presence of UDP-galactose to produce fourth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (a) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (b) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (c) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fourth immobilized N-glycosylated glycoproteins are reacted with a SiaT in the presence of CMP-sialic acid to produce fifth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a 1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third immobilized N-glycosylated glycoproteins are reacted with a GnTIII in the presence of UDP-GlcNAc to produce fourth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a 1-4 linkage to the non-reducing end of the central mannose residue.
In a further embodiment, the fourth immobilized N-glycosylated glycoproteins are reacted with a GalT in the presence of UDP-galactose to produce fifth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked to the non-reducing end of the α1-3-linked mannose residue and a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a 1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fifth immobilized N-glycosylated glycoproteins are reacted with a SiaT in the presence of CMP-sialic acid to produce sixth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-2 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-2 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third immobilized N-glycosylated glycoproteins are reacted with a GnTIV in the presence of UDP-GlcNAc to produce fourth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the fourth immobilized N-glycosylated glycoproteins are reacted with a GalT in the presence of UDP-galactose to produce fifth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue;
(ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; or (iv) a combination of two or more selected from the group consisting of (i), (ii), and (iii).
In a further embodiment, the fifth immobilized N-glycosylated glycoproteins are reacted with a SiaT in the presence of CMP-sialic acid to produce sixth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; or (iv) a combination of two or more selected from the group consisting of (i), (ii), and (iii).
In a further embodiment, the fourth immobilized N-glycosylated glycoproteins are reacted with a GnTV in the presence of UDP-GlcNAc to produce fifth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fifth immobilized N-glycosylated glycoproteins are reacted with a GalT in the presence of UDP-galactose to produce sixth immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue;
(ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; (iv) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue; or (v) a combination of two or more selected from the group consisting of (i), (ii), (iii), and (iv).
In a further embodiment, the sixth immobilized N-glycosylated glycoproteins are reacted with a SiaT in the presence of CMP-sialic acid to produce seventh immobilized N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise
(i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; (iv) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a 1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue; or (v) a combination of two or more selected from the group consisting of (i), (ii), (iii), and (iv).
The present invention further provides a method for remodeling the N-glycans of a composition of N-glycosylated glycoproteins, the steps comprising: (a) providing an aqueous composition of N-glycosylated glycoproteins and two or more solid supports, each solid support having immobilized thereon a multiplicity of glycosylation enzymes and wherein no solid support has immobilized thereon the same multiplicity of glycosylation enzymes; and (b) applying the composition of N-glycosylated glycoproteins sequentially to each solid support for a time sufficient to remodel the N-glycans of the glycoproteins to produce the composition of N-glycosylated glycoproteins comprising remodeled N-glycans. A further step may include separating the composition and purifying the composition.
In a further embodiment, the multiplicity of glycosylation enzymes are irreversibly affixed to the solid support or bound to capture moieties that specifically bind the glycosylation enzymes.
In a further embodiment, the N-glycosylated glycoprotein comprises an antibody or antigen binding fragment.
In a further embodiment, the one or more glycosylation enzymes are selected from the group consisting of exoglycosidases, endoglycosidases, and glycosyltransferases.
In a further embodiment, the exoglycosidases are selected from the group consisting of neuraminidases, galactosidases, fucosidases, and N-acetyl-glucosaminidases; and, the glycosyltransferases are selected from the group consisting of N-acetylglucosaminidyltransferases (GnTs), galactosyltransferases (GalTs), fucosyltransferases (FuTs), and sialyltransferases (SiaTs).
In a further embodiment, the SiaTs are selected from the group consisting of α2-6 SiaT and α2-3 SiaT: the GalTs comprise β1-4GalT: the FuTs comprise α1-6 FuT; and, the GnTs are selected from the group consisting of GnTI, GnTII, GnTIII, GnTIV, and GnTV.
The present invention may use any combination of solid supports comprising a multiplicity of N-glycans immobilized thereon, the combination taking into account the particular characteristics of the glycosylation enzymes.
In a further embodiment, the composition of N-glycosylated glycoproteins are sequentially applied to a solid support comprising a multiplicity of neuraminidases, a solid support comprising a multiplicity of galactosidases, and a solid support comprising a multiplicity of N-acetyl-glucosaminidases to produce a first composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof comprise two terminal mannose residues at the non-reducing end of the N-glycan, one terminal mannose linked to a central mannose residue in an α1-3 linkage and the other terminal mannose linked to the same central mannose in an α1-6 linkage, and the central mannose is linked to a chitobiose core in a β1-4 linkage wherein the GlcNAc residue at the reducing end of the chitobiose core is linked to an asparagine residue of an N-glycosylation site in the N-glycosylated glycoprotein.
In a further embodiment, the first composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GnTIs in the presence of UDP-GlcNAc to produce a second composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the second composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GalTs in the presence of UDP-galactose to produce a third composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the third composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of SiaT in the presence of CMP-sialic acid to produce a fourth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a sialic acid residue linked to the non-reducing end of the galactose residue linked to the non-reducing end of the GlcNAc residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the second composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GnTIIs in the presence of UDP-GlcNAc to produce a third composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GalT in the presence of UDP-galactose to produce a fourth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (a) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a 1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (b) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (c) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fourth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of SiaTs in the presence of CMP-sialic acid to produce a fifth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GnTIIIs in the presence of UDP-GlcNAc to produce a fourth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the central mannose residue.
In a further embodiment, the fourth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GalTs in the presence of UDP-galactose to produce a fifth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a 1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked to the non-reducing end of the α1-3-linked mannose residue and a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fifth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of SiaTs in the presence of CMP-sialic acid to produce a sixth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue, (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue, or (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-2 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue and a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-2 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the third composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GnTIVs in the presence of UDP-GlcNAc to produce a fourth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue.
In a further embodiment, the fourth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GalTs in the presence of UDP-galactose to produce a fifth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a 1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; or (iv) a combination of two or more selected from the group consisting of (i), (ii), and (iii).
In a further embodiment, the fifth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of SiaTs in the presence of CMP-sialic acid to produce a sixth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a 1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; or (iv) a combination of two or more selected from the group consisting of (i), (ii), and (iii).
In a further embodiment, the fourth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GnTVs in the presence of UDP-GlcNAc to produce a fifth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise a GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue.
In a further embodiment, the fifth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of GalTs in the presence of UDP-galactose to produce a sixth composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; (iv) a galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue; or (v) a combination of two or more selected from the group consisting of (i), (ii), (iii), and (iv).
In a further embodiment, the sixth composition of N-glycosylated glycoproteins are applied to a solid support comprising a multiplicity of SiaTs in the presence of CMP-sialic acid to produce a seventh composition of N-glycosylated glycoproteins wherein the remodeled N-glycans thereof further comprise (i) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-3-linked mannose residue; (ii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-2 linkage to the non-reducing end of the α1-6-linked mannose residue; (iii) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-4 linkage to the non-reducing end of the α1-3-linked mannose residue; (v) a sialic acid residue linked in an α2-3 or α2-6 linkage to the non-reducing end of the galactose residue linked in a β1-4 linkage to the non-reducing end of the GlcNAc residue linked in a β1-6 linkage to the non-reducing end of the α1-6-linked mannose residue; or (v) a combination of two or more selected from the group consisting of (i), (ii), (iii), and (iv).
The present invention further provides a method for remodeling the N-glycans of a composition of N-glycosylated glycoproteins, the steps comprising: (a) providing an aqueous composition of N-glycosylated glycoproteins: (b) immobilizing the N-glycosylated glycoproteins on a solid support: (c) reacting the immobilized N-glycosylated glycoproteins with a glycosylation enzyme or sequentially with two or more glycosylation enzymes to produce immobilized N-glycosylated glycoproteins comprising remodeled N-glycans; and (d) eluting the N-glycosylated glycoproteins comprising the remodeled N-glycans from the solid support to provide a composition of the N-glycosylated glycoproteins comprising remodeled N-glycans.
In a further embodiment, the solid support comprises irreversibly affixed thereon a multiplicity of capture moieties that specifically bind the N-glycosylated glycoprotein.
In a further embodiment, the N-glycosylated glycoprotein comprises an antibody or antigen binding fragment.
In a further embodiment, the multiplicity of capture moieties comprises protein A and the N-glycosylated glycoprotein comprises an antibody.
In a further embodiment, the one or more glycosylation enzymes are selected from the group consisting of exoglycosidases, endoglycosidases, and glycosyltransferases.
In a further embodiment, the immobilized N-glycosylated glycoproteins are reacted sequentially with two or more exoglycosidases selected from the group consisting neuraminidases, galactosidases, and an N-acetylglucosaminidases (GlcNAcases) to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans comprising Man3GlcNAc2 N-glycans having the structure
wherein the GlcNAc residue at the reducing end of the Man3GlcNAc2 N-glycans is linked to an asparagine residue forming an N-glycosylation site in the N-glycosylated glycoprotein, wherein Man is mannose and GlcNAc is N-acetylglucosamine.
In a further embodiment, the immobilized N-glycosylated glycoproteins are reacted sequentially with a neuraminidase, a galactosidase, and a GlcNAcase to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans comprising Man3GlcNAc2 N-glycans, wherein the GlcNAc residue at the reducing end of the Man3GlcNAc2 N-glycans is linked to an asparagine residue forming an N-glycosylation site in the N-glycosylated glycoprotein.
In a further embodiment, wherein the immobilized N-glycosylated glycoproteins comprising the Man3GlcNAc2 N-glycans are reacted with an N-acetylglucosaminyltransferase (GnT) I in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal mannose residue of the α1-3 arm is further linked to a GlcNAc residue to produce hybrid GlcNAcMan3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the hybrid GlcNAcMan3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm is further linked to a galactose residue (Gal) to produce hybrid GalGlcNAcMan3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the hybrid GalGlcNAcMan3GlcNAc2 N-glycans are reacted with an α2-6 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm is further linked to a sialic acid residue (Sia) to produce hybrid SiaGalGlcNAcMan3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the hybrid GalGlcNAcMan3GlcNAc2 N-glycans are reacted with an α2-3 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm is further linked to a sialic acid residue (Sia) to produce hybrid SiaGalGlcNAcMan3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the hybrid GlcNAcMan3GlcNAc2 N-glycans are reacted with a GnTII in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal mannose residue of the α1-6 arm is further linked to a GlcNAc residue to produce bi-antennary GlcNAc2Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm and/or terminal GlcNAc residue of the α1-6 arm is further linked to a galactose residue (Gal) to produce bi-antennary GalGlcNAc2Man3GlcNAc2 N-glycans having the structure
bi-antennary Gal2GlcNAc2Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc2Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-6 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc2Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc2Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-3 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a GnTIII in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the central mannose residue is further linked to a GlcNAc residue to produce bisected GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc3Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-glucose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm and/or terminal GlcNAc residue of the α1-6 arm is further linked to a galactose residue (Gal) to produce bi-antennary GalGlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Gal2GlcNAc3Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc3Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-6 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc3Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc3Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc3Man3GlcNAc2 N-glycans are reacted with an α2-3 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins are reacted with one exoglycosidase or sequentially with two or more exoglycosidases to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans comprising GlcNAc2Man3GlcNAc2 N-glycans having the structure
wherein the GlcNAc residue at the reducing end of the GlcNAc2Man3GlcNAc2 N-glycans is linked to an asparagine residue forming an N-glycosylation site in the N-glycosylated glycoprotein, wherein Man is mannose and GlcNAc is N-acetylglucosamine.
In a further embodiment, the immobilized N-glycosylated glycoproteins are reacted sequentially with a neuraminidase and a galactosidase to produce a population of glycoproteins comprising remodeled N-glycans comprising the GlcNAc2Man3GlcNAc2 N-glycans, wherein the GlcNAc residue at the reducing end of the GlcNAc2Man3GlcNAc2 N-glycans is linked to an asparagine residue forming an N-glycosylation site in the N-glycosylated glycoprotein.
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm and/or terminal GlcNAc residue of the α1-6 arm is further linked to a galactose residue (Gal) to produce bi-antennary GalGlcNAc2Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc2Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-6 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue (Gal) of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc2Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GalGlcNAc2Man3GlcNAc2 and/or bi-antennary Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-3 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bi-antennary SiaGal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
and/or bi-antennary Sia2Gal2GlcNAc2Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a GnTIII in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the central mannose residue is further linked to a GlcNAc residue to produce bisected GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bisected GlcNAc3Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm and/or terminal GlcNAc residue of the α1-6 arm is further linked to a galactose residue (Gal) to produce bisected GalGlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bisected Gal2GlcNAc3Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bisected GalGlcNAc3Man3GlcNAc2 and/or bisected Gal2GlcNAc2Man3GlcNAc2 N-glycans are reacted with an α2-6 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bisected SiaGal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bisected Sia2Gal2GlcNAc3Man3GlcNAc2N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bisected GalGlcNAc3Man3GlcNAc2 and/or bisected Gal2GlcNAc3Man3GlcNAc2 N-glycans are reacted with an α2-3 sialyltransferase (SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm and/or terminal galactose residue of the α1-6 arm is further linked to a sialic acid residue (Sia) to produce bisected SiaGal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
and/or bisected Sia2Gal2GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a GnTIV in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the mannose residue of the α1-3 arm is further linked to a GlcNAc residue to produce α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, or all three of the terminal GlcNAc residues is further linked to a galactose residue (Gal) to produce α1-3 tri-antennary Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans, which structure represents that any one or two terminal GlcNAc residues are each linked to galactose, or all three terminal GlcNAc residues are each linked to galactose.
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the α1-3 arm tri-antennary Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans are reacted with an α2-6-sialyltransferase (α2-6-SiaT) or α2-3 sialyltransferase (α2-3-SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, or all three of the terminal galactose residues is/are further linked to a sialic acid residue (Sia) to produce α2-6-Sia, α1-6 arm tri-antennary Sia(1-3)Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans or α2-3-Sia, α1-6 arm tri-antennary Sia(1-3)Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans, respectively, which structure represents that any one or two terminal galactose residues are each linked to sialic acid, or all three terminal galactose residues are each linked to sialic acid.
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the bi-antennary GlcNAc2Man3GlcNAc2 N-glycans are reacted with a GnTV in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the mannose residue of the α1-6 arm is linked to a GlcNAc residue to produce α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, or all three of the terminal GlcNAc residues is/are further linked to a galactose residue (Gal) to produce α1-6 arm tri-antennary Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans, which structure represents any one or two terminal GlcNAc residues are each linked to galactose, or all three terminal GlcNAc residues are each linked to galactose.
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the α1-6 arm tri-antennary Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans are reacted with an α2-6-sialyltransferase (α2-6-SiaT) or α2-3 sialyltransferase (α2-3-SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, or all three of the terminal galactose residues is/are further linked to a sialic acid residue (Sia) to produce α2-6-Sia, α1-6 arm tri-antennary Sia(1-3)Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans or α2-3-Sia, α1-6 arm tri-antennary Sia(1-3)Gal(1-3)GlcNAc3Man3GlcNAc2 N-glycans, respectively, which structure represents any one or two terminal galactose residues are each linked to sialic acid, or all three terminal galactose residues are each linked to sialic acid.
In a further embodiment, (i) the immobilized N-glycosylated glycoproteins comprising the α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans is further reacted with a GnTV in the presence of UDP-GlcNAc or (ii) the immobilized N-glycosylated glycoproteins comprising the α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans is further reacted with a GnTIV in the presence of UDP-GlcNAc, to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the mannose residues of the α1-3 arm and α1-6 arm are each further linked to a GlcNAc residue to produce multi-antennary GlcNAc4Man3GlcNAc2 N-glycans having the structure
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the multi-antennary GlcNAc4Man3GlcNAc2 N-glycans are reacted with a β1-4 galactosyltransferase (GalT) in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, three, or all four of the terminal GlcNAc residues is/are further linked to a galactose residue (Gal) to produce Gal(1-4)GlcNAc4Man3GlcNAc2 N-glycans, which structure represents any one, two, or three terminal GlcNAc residues are each linked to galactose, or all four terminal GlcNAc residues are each linked to galactose.
In a further embodiment, the immobilized N-glycosylated glycoproteins comprising the α1-6 arm multi-antennary Gal(1-4)GlcNAc4Man3GlcNAc2 N-glycans are reacted with an α2-6-sialyltransferase (α2-6-SiaT) or α2-3 sialyltransferase (α2-3-SiaT) in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which one, two, three, or all four of the terminal galactose residues is/are further linked to a sialic acid residue (Sia) to produce α2-6-Sia multi-antennary Sia(1-4)Gal(1-4)GlcNAc4Man3GlcNAc2 N-glycans or α2-3-Sia multi-antennary Sia(1-4)Gal(1-4)GlcNAc4Man3GlcNAc2 N-glycans, respectively, which structure represents any one, two, or three terminal galactose residues are each linked to sialic acid, or all four terminal galactose residues are each linked to sialic acid.
As used herein, the Oxford notation name is used for glycan nomenclature and the glycan structures are presented according to the Consortium for Functional Glycomics (CFG). As used herein, the term “glycosylation enzymes” refers to exoglycosidases, endoglycosidases, and glycosyltransferases, and includes both native and naturally occurring enzymes and recombinant variants thereof that comprise at least the catalytic activity of the glycosylation enzyme.
As used herein, the term “exoglycosidases” are glycoside hydrolase enzymes (EC 3.2) that cleave the glycosidic linkage of a terminal monosaccharide in an oligosaccharide or polysaccharide. Exoglycosidases include neuraminidases, galactosidases, N-acetylglucosaminidases, and fucosidases.
As used herein, “endoglycosidases” are glycoside hydrolase enzymes (EC 3.2) that cleave the glycosidic linkage between the two N-acetylglucosamine (GlcNAc) residues of the chitobiose core, but which recognize and cleave different types of N-linked glycans. For example, endoglycosidase H cleaves within the chitobiose core of high mannose and some hybrid oligosaccharides from N-linked glycoproteins, endoglycosidase S is highly specific for removing N-linked glycans from the heavy chain of native IgG, and endoglycosidase D cleaves paucimannose N-linked glycans.
As used herein, “glycosyltransferases” are enzymes (EC 2.4) that catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the “glycosyl donor”) to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen-carbon-, nitrogen-, or sulfur-based. Examples of glycosyltransferases include but are not limited to N-acetylglucosaminyltransferase (GnT) I, which transfers GlcNAc from UDP-GlcNAc to the α1,3-linked terminal mannose (Man) residue on paucimannose N-glycans; GnTII, which transfers GlcNAc from UDP-GlcNAc to the α1,6-linked terminal mannose of GlcNAcMan3GlcNAc2 N-glycans in a β1-2 linkage; GnTIII, which transfers GlcNAc from UDP-GlcNAc to the α1,4-linked central mannose of GlcNAcMan3GlcNAc2 N-glycans in a β1-4 linkage; β1,4-galactosyltransferase (GalT), which transfers galactose (Gal) from UDP-galactose to the terminal GlcNAc residues of N-glycans in a β1-4 linkage; α2,3-sialyltransferase (α2,3-sialyIT) or α2,6-sialyltransferase (α2,6-sialyIT), which transfers sialic acid from CMP-sialic acid to the terminal galactose residues of N-glycans in an α2-6 linkage; α2,3-sialyltransferase (α2,3-sialyIT), which transfers sialic acid from CMP-sialic acid to the terminal galactose residues of N-glycans in an α2-3 linkage; and, α1,6-fucosyltransferase (FUT8) transfers fucose from GDP-fucose to the GlcNAc residue at the reducing end of the chitobiose core in an α1,6 linkage.
As used herein, the term “N-glycan” refers to an N-linked oligosaccharide, e.g., one that is attached by an asparagine-N-acetylglucosamine linkage to an asparagine residue of a polypeptide. 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). The term “trimannose core” or “paucimannose core” used with respect to the N-glycan also refers to the structure Man3GlcNAc2 (“Man3”). N-glycans differ with respect to the number of branches (antennae) comprising peripheral sugars (e.g., fucose and sialic acid) that are added to the Man3 core structure. 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 α1,3 mannose arm and at least one GlcNAc attached to the α1,6 mannose arm of the trimannose core. Complex N-glycans may also have galactose (“Gal”) residues that are optionally modified with sialic acid or derivatives (“NeuAc”, where “Neu” refers to neuraminic acid and “Ac” refers to acetyl). Complex N-glycans may also have intrachain substitutions comprising “bisecting” GlcNAc and core fucose (“Fuc”). A “hybrid” N-glycan has at least one GlcNAc on the terminal of the α1,3 mannose arm of the trimannose core and zero or more mannoses on the α1,6 mannose arm of the trimannose core.
As used herein, the term “predominant” or “predominantly” used with respect to the production of N-glycans refers to a structure which represents the major peak detected by ultrahigh pressure liquid chromatography with ultraviolet (UPLC-UV) absorbance measurement. Glycan masses were confirmed with UPLC interfaced to electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF-MS).
As used herein, the term “multiplicity” refers to a large number of the same or substantially same molecules, proteins, enzymes, species, etc. For example, a multiplicity of glycoproteins refers to a population of glycoproteins in which the glycoproteins have the same amino acid sequence and the same N-glycan structure. For example, a multiplicity of glycoproteins refers to a population of glycoproteins wherein the glycoproteins have substantially the same amino acid sequence and the N-glycans have substantially the same structure.
As used herein, the term “plurality” refers to a large number of a variety of species of molecules, proteins, enzymes, species, etc. For example, a plurality of glycoproteins refers to (i) a population of glycoproteins in which the glycoproteins have substantially the same amino acid sequence and more than one N-glycan structure. e.g., N-glycans comprising a mixture of Sia(1-2)Gal(1-2)GlcNAc(1-2)Man3GclNAc2, Gal(1-2)GlcNAc(1-2)Man3GclNAc2, and GlcNAc(1-2)Man3GclNAc2 structures, or (ii) a population of glycoproteins in which the glycoproteins comprise more than one amino acid sequence and a single N-glycan structure or more than one N-glycan structure.
As used herein, the term “sequentially” refers to forming or following in a logical order or sequence. For example, a glycoprotein may be reacted with a neuraminidase, a galactosidase, and a GlcNAcase in that order to produce a paucimannose N-glycan.
As used herein, the term “remodel” or “remodeling” refers to changing the structure of an N-glycan having a particular glycoform to another glycoform, by removing and/or adding sugar residues to the N-glycan. The term further includes changing the structures of the N-glycans of a population of glycoproteins.
Abbreviations used herein are of common usage in the art, see, e.g., abbreviations of sugars, above.
The present invention provides a solid-phase glycan remodeling (“SPGR”) system wherein glycosylation enzymatic reactions are carried out on glycoprotein substrates immobilized on solid supports. The SPGR system enables efficient reaction swapping, substrate purification, and the recovery of both remodeled glycosylated glycoprotein products and the glycosylation engineering enzymes. The SPGR system is particularly useful for glycoengineering immunoglobulins (antibodies or IgG) to provide antibodies that have predominantly particular glycoform profiles. The SPGR system enables harmonization of antibody glycans into one or more of ten different glycoforms, including non-canonical structures, in 48 hours with an averaged conversion ratio greater than 95%. Physical and biochemical analyses indicate that the SPGR-engineered antibodies preserved integrity and functionality, suggesting that the SPGR system has high biocompatibility to the antibody substrates.
For decades there has been a clear demand for glycoengineering tools that enable the production of glycoproteins having particular glycoforms for therapeutic uses as well as evaluating the role(s) of glycan structures on the function and form of glycoconjugates. SPGR of the present invention presents a straightforward strategy for controlling glycan structures with several advantages: 1) it is a biocompatible approach with minimal disruption to the protein substrates: 2) it circumvents the need to prepare synthetic glycans, which can be cumbersome: 3) tight control of glycoforms is achievable with the use of different enzyme combinations and: 4) the procedures are user-friendly and can be readily automated to greatly increase efficiency for industrial applications. Moreover, the idea of executing sequential enzymatic remodeling on immobilized proteins can potentially be extended to most existing biocatalytic cascade reactions involving different classes of enzymes and substrates (Huffman et al., Science 366, 1255-1259, doi: 10.1126/science.aay8484 (2019)).
A particularly disruptive application of SPGR of the present invention would be to humanize glycoforms on therapeutic proteins produced from non-human cell lines. Chinese hamster ovary (CHO) cells are commonly used for therapeutic protein production because they generate human-like post-translational modifications (Walsh, Nature Biotechnology 28, 917-924, doi: 10.1038/nbt0910-917 (2010)). However, non-human glycoforms still exist in the cell line and to reduce the potential immune response in patients, these non-human glycoforms should be removed (Liu et al. PLOS One 12, e0170013-e0170013, doi: 10.1371/journal.pone.0170013 (2017)). SPGR can be employed to humanize those glycans during the production process. From a different perspective, protein production in mammalian hosts is costly because of the long fermentation time and liability of virus infections. To address this issue, yeast has been employed as an alternative host for large-scale expression of therapeutic proteins. Glycoproteins expressed from yeast contain high-mannose N-glycans which confer a short half-life in vivo and thereby compromise the efficacy of most therapeutic proteins (Goetze et al., Glycobiology 21, 949-959, doi: 10.1093/glycob/cwr027 (2011)). Therefore, gene engineered strains are constructed for producing human-mimicking glycan patterns (Wildt & Gerngross, Nat Rev Microbiol 3, 119-128, doi: 10.1038/nrmicro1087 (2005); Laukens et al., Future Microbiol 10, 21-34, doi: 10.2217/fmb.14.104 (2015)). To date, several glycoforms have been achieved in yeast and they have provided the desired scaffold (e.g., M3 or M5 glycan and mixtures of complex N-glycans) for downstream glycan remodeling in vitro (Liu et al. Proc Natl Acad Sci USA 115, 720-725, doi: 10.1073/pnas. 1718172115 (2018)). With the combination of SPGR of the present invention, large-scale production of therapeutic proteins in yeast with controlled glycan structures is possible.
The awareness of public health has been raised significantly in the past months, intensifying the demand for developing better biologic medicines. Glycoproteins are established foundational entities in biologic medicine and vaccine development, which stresses the urgent need for exquisite control of glycosylation profiles for improved safety and efficacy. The present invention presents an efficient, user-friendly method for glycoengineering. It enables the control of glycan structures with various glycoforms and, presumably, on diverse glycoproteins.
The SPGR system of the present invention enables efficient reaction swapping, substrate purification, and the recovery of both products and engineering enzymes (Palomo, RSC Advances 4, 32658-32672, doi: 10.1039/C4RA02458C (2014); Coin et al., Nature Protocols 2, 3247-3256, doi: 10.1038/nprot.2007.454 (2007)). The present invention is particularly useful for glycoengineering antibodies. We quantitatively examined more than 30 glycan engineering enzymes for their activities on intact IgG immobilized on resins and then applied them in SPGR. This method has allowed us to harmonize IgG glycans into ten different glycoforms, including non-canonical structures, in 48 hours with an averaged conversion ratio greater than 95%. Physical and biochemical analyses indicated that the SPGR-engineered IgGs preserved integrity and functionality, suggesting that SPGR has high biocompatibility to the substrates.
In general, the SPGR system of the present invention provides a means for remodeling the N-glycans of a composition of glycoproteins comprising a heterogenous mixture or population of glycoforms, including non-human glycoforms, into a relatively homogenous mixture of glycoforms or human glycoforms as follows.
A composition of glycoproteins comprising N-glycans having a plurality of glycoforms is applied to a solid support under conditions in which the glycoproteins are reversibly immobilized on the solid support. The immobilized glycoproteins are then (i) reacted with a solution comprising a glycosylation enzyme to add or remove a sugar residue from particular or all N-glycans in the population, (ii) reacted successively with solutions of particular glycosylation enzymes to remove one or more sugar residues from particular N-glycans or all N-glycans, (iii) reacted successively with solutions comprising particular glycosylation enzymes to remove one or more sugar residues from particular N-glycans or all N-glycans and then reacted successively with solutions comprising one or more glycosylation enzymes to add one or more sugar residues to particular N-glycans or N-glycans. In embodiments where there are multiple successive removal and/or addition of sugar residues steps, between each reaction step there may be a buffer exchange step in which the reaction solution for the previous reaction step is removed and replaced with a reaction buffer for the subsequent step. Following the final reaction step, the reaction solution is removed and the immobilized glycoproteins are eluted from the solid support under conditions that disrupt the binding of the glycoprotein to the solid support to provide a composition comprising glycoproteins having remodeled N-glycans.
In particular embodiments, the glycoproteins are sequentially reacted with one or more glycosidases, to remove one or more terminal sugars on the N-glycan. For example, in a first step, the glycoproteins are reacted with a first glycosidase specific for a first sugar residue at the terminus of an N-glycan. The first glycosidase removes the particular sugar residue from the termini of those N-glycans that comprise said terminal sugar residue to expose a second sugar residue at the termini of those N-glycans to provide a population of N-glycans comprising terminal second sugar residues. In a second step, the glycoproteins may then be reacted with a second glycosidase that is specific for the second sugar residue at the terminus of an N-glycan. The second glycosidase removes the second sugar residue at the termini of those N-glycans reacted with the first glycosidase and any other N-glycans that comprise the second sugar residue at the terminus to expose a third sugar residue at the termini of the N-glycans to provide a population of N-glycans comprising terminal third sugar residues. In a third step, the glycoproteins may then be reacted with a third glycosidase that is specific for third sugar residue at the terminus of an N-glycan. The third glycosidase removes the third sugar residue at the termini of those N-glycans reacted with the second glycosidase and any other N-glycans that comprise the third sugar residue at the terminus to expose a fourth sugar residue at the termini of the N-glycans to provide a population of N-glycans comprising terminal fourth sugar residues. For glycoproteins produced in mammalian or human cells, the glycoproteins may be reacted with a fucosidase which removes the sugar residue fucose from N-glycans.
In a further embodiment, following any one of the above steps, the population of N-glycans may be reacted with a glycosyltransferase capable of adding a specific sugar to the terminal sugar residues of a particular population of N-glycans. Successive reactions, each utilizing a specific glycosyltransferase, may be used to add successive sugars to the termini of the N-glycans to produce a population of N-glycans having particular glycoforms. In particular embodiments, the glycoforms comprising the population of N-glycans are homogenous or comprise a mixture of glycoforms wherein one or more glycoforms are predominant.
Glycoproteins produced in mammalian cells have complex N-glycans, which depending on the cell-type and the glycoprotein can have a vast array of glycoforms in differing amounts, including fucosylated and non-fucosylated bi-antennary, bisected, tri-antennary, and multi-antennary glycoforms comprising terminal sialic acid, galactose, or GlcNAc residues, or combinations thereof (for example,
Mammalian and human complex N-glycans comprise GlcNAc, mannose, galactose, and sialic acid residues. Complex N-glycans comprise a paucimannose core represented by the formula Man3GlcNAc2 forming a Y-shaped molecule wherein the terminal mannose residues are on the distal end of the chitobiose core and the GlcNAc residue at the reducing end of the chitobiose core is linked to asparagine (Asn) in a β1-N linkage. The terminal mannose residues are linked by α1-6 and α1-3 linkages to a central mannose residue to provide an α1-6-linked mannose arm and an α1-3-linked mannose arm. The central mannose is in turn linked to the chitobiose core by a β1-4 linkage. Terminal GlcNAc residues, when present, are linked to the terminal mannose residue on the α1-3-linked mannose arm in a β1-2 linkage by GnTI to produce hybrid N-glycans, and then to the terminal mannose residue on the α1-6 linked arm by GnTII to produce bi-antennary N-glycans. An additional GlcNAc residue, when present, may be linked to the terminal mannose residue on the α1-3-linked mannose arm of bi-antennary N-glycans in a β1-4 linkage by GnTIV or the terminal mannose residue on the α1-6-linked mannose arm of bi-antennary N-glycans in a β1-6 linkage by GnTV to produce tri-antennary N-glycans. In a further aspect, a GlcNAc residue, when present, may be linked to the arm of the tri-antennary N-glycan that is linked to only one GlcNAc residue with the appropriate GnT to produce multi-antennary N-glycans in which each arm comprises two GlcNAc residues, the α1-3-linked mannose arm comprising GlcNAc residues linked in a β1-2 linkage and a β1-4 linkage and the α1-6-linked mannose arm comprising GlcNAc residues linked in a β1-2 linkage and a β1-6 linkage. In an alternate aspect, the central mannose of bi-antennary N-glycans may be linked to a GlcNAc residue by a β1-4 linkage by GnTIII to produce bisected N-glycans. Terminal galactose residues, when present, are linked to the terminal GlcNAc residues of bi-antennary, tri-antennary, or multi-antennary N-glycans in a β1-4 linkage by GalT or to the α1-6-linked mannose arm and an α1-3-linked mannose arm GlcNAc residues of bisected N-glycans in a β1-4 linkage by GalT. Terminal sialic acid residues, when present, are linked to one or more of the terminal galactose residues of any of the bi-antennary, tri-antennary, multi-antennary, or bisected N-glycans comprising terminal galactose residues in either an α2-3 or α2-6 linkage by α2,3-siaT or α2,6-siaT, respectively, to produce α2,3- or α2,6-sialylated N-glycans. In particular embodiments, the sialic acid is N-Acetylneuraminic acid (Neu5Ac or NANA), a predominant sialic acid found in human cells and many mammalian cells.
Thus, in particular embodiments, the N-glycosylated glycoproteins are sequentially reacted with one or more glycosidases selected from group consisting of neuraminidase, galactosidase, and N-acetylglucosaminidase, to remove one or more terminal sugar residues on the N-glycan to produce a core structure. For example, in a first step, the glycoproteins are reacted with one or more neuraminidases to remove the sialic acid residues from those N-glycans that comprise terminal sialic acid residues to provide a population of N-glycans comprising terminal galactose residues. In a second step, the glycoproteins may then be reacted with one or more galactosidases that remove the galactose residues from those N-glycans that comprise terminal galactose residues to provide a population of N-glycans comprising terminal GlcNAc residues. In a third step, the glycoproteins may then be reacted with one or more N-acetylglucosaminidases that remove the GlcNAc residues from those N-glycans that comprise terminal galactose residues to provide a population of paucimannose N-glycans (Man3GlcNAc2), each N-glycan comprising a central mannose residue linked to a chitobiose core in a β1-4 linkage and two terminal mannose residues, one linked to the central mannose in an α1,3 linkage and the other linked to the central mannose in an α1,6 linkage. After any one of the three steps, the glycoproteins may be further reacted with a fucosidase to remove fucose residues from those the N-glycans comprising a fucose linked to the GlcNAc residue at the reducing end of the chitobiose core in an α1,6 linkage.
In a further embodiment, following any one of the above three steps, the population of N-glycans may be reacted with a glycosyltransferase capable of adding a specific sugar to the terminal sugar residues of a particular population of N-glycans. Successive reactions, each utilizing a specific glycosyltransferase, may be used to add sugars to the termini of the N-glycans in a stepwise manner to produce a population of N-glycans having particular glycoforms. The particular glycosyltransferase that may be used in a particular reaction will depend on the N-glycan substrate to be reacted upon by the glycosyltransferase as each glycosyltransferase is specific for a particular substrate.
Thus, in one embodiment of the present invention, a population of glycoproteins comprising Man3GlcNAc2 N-glycans may be reacted with an GnTI in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising hybrid GlcNAcMan3GlcNAc2 N-glycans in which the α1,3-linked mannose residue is linked to a GlcNAc residue by a β1-2 linkage. The population of glycoproteins comprising hybrid GlcNAcMan3GlcNAc2 N-glycans may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising hybrid GalGlcNAcMan3GlcNAc2 N-glycans in which galactose is linked to the GlcNAc residue in a β1-4 linkage. The population of glycoproteins comprising hybrid GalGlcNAcMan3GlcNAc2 N-glycans may then be reacted with a α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising hybrid SiaGalGlcNAcMan3GlcNAc2 N-glycans in which sialic acid is linked to the galactose residue in an α2-6 or α2-3 linkage, respectively.
In another embodiment of the present invention, a population of glycoproteins comprising Man3GlcNAc2 N-glycans may be reacted with an GnTI in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising hybrid GlcNAcMan3GlcNAc2 N-glycans in which the α1,3-linked mannose residue is linked to a GlcNAc residue by a β1-2 linkage. The population of glycoproteins comprising hybrid GlcNAcMan3GlcNAc2 N-glycans may then be reacted with an GnTII in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising bi-antennary GlcNAc2Man3GlcNAc2 N-glycans in which the α1,6-linked mannose residue is linked to a GlcNAc residue by a β1-2 linkage. The population of glycoproteins comprising bi-antennary GlcNAc2Man3GlcNAc2 may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising bi-antennary Gal1-2GlcNAc2Man3GlcNAc2 N-glycans in which galactose is linked to one or both GlcNAc residues in a β1-4 linkage. The population of glycoproteins comprising bi-antennary Gal1-2GlcNAc2Man3GlcNAc2 may then be reacted with a α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising bi-antennary Sia1-2Gal1-2GlcNAc2Man3GlcNAc2 N-glycans in which sialic acid is linked to one or both galactose residues of bi-antennary Gal1-2GlcNAc2Man3GlcNAc2 in an α2-6 or α2-3 linkage, respectively.
In another embodiment of the present invention, a population of glycoproteins comprising bi-antennary GlcNac2Man3GlcNAc2 N-glycans may be reacted with an GnTIII in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising bisected GlcNAc3Man3GlcNAc2 N-glycans in which the central mannose residue is linked to a GlcNAc residue by a β1-4 linkage. The population of glycoproteins comprising bisected GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising bisected Gal1-2GlcNAc3Man3GlcNAc2 N-glycans in which galactose is linked to one or both of the terminal GlcNAc residues on the α1-3 arm or the α1-6 arm in β1-4 linkages. The population of glycoproteins comprising bisected Gal1-2GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with a α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising bisected Sia1-2Gal1-2GlcNAc3Man3GlcNAc2 N-glycans in which sialic acid is linked to one or both of the terminal galactose residues in α2-6 or α2-3 linkages, respectively.
In another embodiment of the present invention, a population of glycoproteins comprising bi-antennary GlcNac2Man3GlcNAc2 N-glycans may be reacted with an GnTIV in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans in which the mannose residue on the α1-3 arm is further linked to a GlcNAc residue by a β1-4 linkage. The population of glycoproteins comprising the α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising α1-3 arm tri-antennary Gal1-3GlcNAc3Man3GlcNAc2 N-glycans in which galactose is linked to one, two, or three of the terminal GlcNAc residues in β1-4 linkages. The population of glycoproteins comprising α1-3 arm tri-antennary Gal1-3GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with an α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising α1-3 arm tri-antennary Sia1-3Gal1-3GlcNAc3Man3GlcNAc2 N-glycans in which sialic acid is linked to one, two, or three of the terminal galactose residues in α2-6 or α2-3 linkages, respectively.
In another embodiment of the present invention, a population of glycoproteins comprising bi-antennary GlcNac2Man3GlcNAc2 N-glycans may be reacted with an GnTV in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans in which the mannose residue on the α1-6 arm is further linked to a GlcNAc residue by a β1-4 linkage. The population of glycoproteins comprising the α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising α1-6 arm tri-antennary Gal1-3GlcNAc3Man3GlcNAc2 N-glycans in which galactose is linked to one, two, or three of the terminal GlcNAc residues in β1-4 linkages. The population of glycoproteins comprising α1-6 arm tri-antennary Gal1-3GlcNAc3Man3GlcNAc2 N-glycans may then be reacted with a α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising α1-6 arm tri-antennary Sia1-3Gal1-3GlcNAc3Man3GlcNAc2 N-glycans in which sialic acid is linked to one, two, or three of the terminal galactose residues in α2-6 or α2-3 linkages, respectively.
In another embodiment of the present invention, (i) a population of glycoproteins comprising α1-3 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans may be reacted with GnTV in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising multi-antennary GlcNAc4Man3GlcNAc2 N-glycans in which the mannose residues on the α1-6 arm is further linked to a GlcNAc residue by a β1-6 linkage or (ii) a population of glycoproteins comprising α1-6 arm tri-antennary GlcNAc3Man3GlcNAc2 N-glycans may be reacted with GnTIV in the presence of UDP-GlcNAc to produce a population of glycoproteins comprising multi-antennary GlcNAc4Man3GlcNAc2 N-glycans in which the mannose residues on the α1-3 arm is further linked to a GlcNAc residue by a β1-4 linkage. The population of glycoproteins comprising the multi-antennary GlcNAc4Man3GlcNAc2 N-glycans may then be reacted with a GalT in the presence of UDP-galactose to produce a population of glycoproteins comprising α1-3 arm tri-antennary Gal1-4GlcNAc4Man3GlcNAc2 N-glycans in which galactose is linked to one or both GlcNAc residues in a β1-4 linkage. The population of glycoproteins comprising α1-3 arm tri-antennary Gal1-4GlcNAc4Man4GlcNAc2 N-glycans may then be reacted with a α2,6- or α2,3-siaT in the presence of CMP-sialic acid to produce a population of glycoproteins comprising α1-3 arm tri-antennary Sia1-4Gal1-4GlcNAc4Man3GlcNAc2 N-glycans in which sialic acid is linked to one or both galactose residues in an α2-6 or α2-3 linkage, respectively.
In particular embodiments of the present invention, the population of glycoproteins may comprise non-complex N-glycans such as the hypermannosylated or highly mannosylated N-glycans in yeast or filamentous fungi. Non-complex N-glycans lack the GlcNAc, Sialic acid, galactose, and fucose residues that comprise the complex N-glycans of human or mammalian glycoproteins. Glycoproteins comprising non-complex N-glycans may be remodeled using the SPGR process of the present invention provided yeast cells for producing the glycoproteins are genetically modified to produce N-glycans to reduce or eliminate the production of hyper or highly mannosylated N-glycans.
Yeast such as Saccharomyces cerevisiae and Pichia pastoris produce N-glycans that are hypermannosylated or highly mannosylated. In addition, Pichia pastoris produces N-glycans that may comprise phosphorylated N-glycans. To inhibit high or hypermannosylation, the yeast cell may be selected or engineered to be depleted in α1,6-mannosyl transferase activities, which would otherwise add mannose residues onto the N-glycan on a glycoprotein. For example, in yeast such an al, 6-mannosyl transferase activity is encoded by the OCHI gene and deletion or disruption of expression of the OCHI gene (och1Δ) inhibits the production of high mannose or hypermannosylated N-glycans in yeast such as Pichia pastoris or Saccharomyces cerevisiae. (See for example, Gerngross et al. in U.S. Pat. No. 7,029,872: Contreras et al. in U.S. Pat. No. 6,803,225; and Chiba et al. in EP1211310B1 the disclosures of which are incorporated herein by reference).
To reduce or eliminate the likelihood of N-glycans with β-linked mannose residues, which are resistant to α-mannosidases, the recombinant glycoengineered Pichia pastoris host cells are genetically engineered to eliminate glycoproteins having α-mannosidase-resistant N-glycans by deleting or disrupting one or more of the β-mannosyltransferase genes (e.g., BMT1, BMT2. BMT3, and BMT4) (See, U.S. Pat. Nos. 7,465,577, 7,713,719, and Published International Application No. WO2011046855, each of which is incorporated herein by reference). The deletion or disruption of BMT2 and one or more of BMT1, BMT3, and BMT4 also reduces or eliminates detectable cross reactivity to antibodies against host cell protein.
In such cells that lack expression of the OCHI gene and one or more of the BMT genes may be used to produce glycoproteins that have non-complex N-glycans. The glycoproteins may then be immobilized on a solid support and reacted with one or more mannosidases to produce a population of glycoproteins comprising paucimannose N-glycans. The glycoproteins comprising the paucimannose N-glycans may then be further reacted as described above to make populations of N-glycans with a desired N-glycan structures.
In an embodiment of the invention, a population of glycoproteins obtained from yeast host cells that lack OCHI and/or BMT activity comprising Man8GlcNAc2 N-glycans having the structure
are reacted with a solution comprising one or mannosidases that remove α1-2-linked mannose residues, to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans comprising Man5GlcNAc2 N-glycans having the structure
In a further embodiment, wherein the N-glycosylated glycoproteins comprising the Man5GlcNAc2 N-glycans are reacted with GnTI in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal mannose residue of the α1-3 arm is further linked to a GlcNAc residue to produce hybrid GlcNAcMan5GlcNAc2 N-glycans having the structure
In a further embodiment, the N-glycosylated glycoproteins comprising the hybrid GlcNAcMan5GlcNAc2 N-glycans are reacted with a GalT in the presence of UDP-galactose to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal GlcNAc residue of the α1-3 arm is further linked to a galactose residue to produce hybrid GalGlcNAcMan5GlcNAc2 N-glycans having the structure
In a further embodiment, the N-glycosylated glycoproteins comprising the hybrid GalGlcNAcMan5GlcNAc2 N-glycans are reacted with an α2-6-SiaT in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm is further linked to a sialic acid residue to produce hybrid SiaGalGlcNAcMan5GlcNAc2 N-glycans having the structure
In a further embodiment, the N-glycosylated glycoproteins comprising the hybrid GalGlcNAcMan5GlcNAc2 N-glycans are reacted with an α2-3-SiaT in the presence of CMP-sialic acid to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal galactose residue of the α1-3 arm is further linked to a sialic acid residue to produce hybrid SiaGalGlcNAcMan5GlcNAc2 N-glycans having the structure
In a further embodiment, the N-glycosylated glycoproteins comprising the hybrid GlcNAcMan5GlcNAc2 N-glycans are reacted with a mannosidase II to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal mannose residues of the α1-6 arm are removed to produce hybrid GlcNAcMan3GlcNAc2 N-glycans having the structure
In further embodiments, the N-glycosylated glycoproteins comprising hybrid GlcNAcMan3GlcNAc2 N-glycans may be remodeled as disclosed supra to produce galactose-terminated or sialic acid terminated hybrid N-glycans.
In a further embodiment, the N-glycosylated glycoproteins comprising the hybrid GlcNAcMan3GlcNAc2 N-glycans are reacted with a GnTII in the presence of UDP-GlcNAc to produce a population of N-glycosylated glycoproteins comprising remodeled N-glycans in which the terminal mannose residue of the α1-6 arm is further linked to a GlcNAc residue to produce bi-antennary GlcNAc2Man3GlcNAc2 N-glycans having the structure
In further embodiments, the N-glycosylated glycoproteins comprising bi-antennary GlcNAc2Man3GlcNAc2 N-glycans may be remodeled as disclosed supra to produce galactose-terminated and/or sialic acid terminated bi-antennary N-glycans.
In particular embodiments of the invention, the glycoforms comprising the population of remodeled N-glycans are homogenous or comprise a mixture of glycoforms wherein one glycoform is predominant. In particular embodiments, the predominant glycoform comprises at least 90% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, the predominant glycoform comprises at least 80% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, the predominant glycoform comprises at least 70% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, the predominant glycoform comprises at least 60% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, the predominant glycoform comprises at least 50% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, the remodeled N-glycans comprise only one detectable glycoform.
In particular embodiments of the invention, the glycoforms comprising the population of remodeled N-glycans comprise a mixture of glycoforms wherein two or three glycoforms comprise at least 50% of the glycoforms in the population of remodeled N-glycans. In particular embodiments, at least 60% of the glycoforms of the remodeled N-glycans comprise two or three glycoforms. In particular embodiments, at least 70% of the glycoforms of the remodeled N-glycans comprise two or three glycoforms. In particular embodiments, at least 80% of the glycoforms of the remodeled N-glycans comprise two or three glycoforms. In particular embodiments, at least 90% of the glycoforms of the remodeled N-glycans comprise two or three glycoforms. In particular embodiments, the detectable glycoforms of the remodeled N-glycans comprise two or three glycoforms.
In particular embodiments, populations of glycoproteins comprising any one of the above hybrid or complex N-glycans may be reacted with an α1-6-fucosyltransferase, which transfers a fucose residue from GDP-fucose to the GlcNAc residue on the reducing end of the chitobiose core in an α1-6 linkage.
Glycosylation enzymes include exoglycosidases, endoglycosidases, and glycosyltransferases, many of which are type-II membrane proteins. The SPGR process of the present invention may be performed using any glycosylation enzyme know in the art when used under conditions suitable for enzyme activity. Many glycosylation enzymes are commercially available whereas others are encoded by nucleotide sequences that are available in the art and can be cloned and synthesized in vitro using well-known molecular biology techniques. As used herein, a glycosylation enzyme may be a recombinant enzyme that comprises the catalytic domain of the enzyme and lacks the transmembrane and/or native signal or leader domains.
The Repository for Glyco-enzyme Expression Constructs located at the Complex Carbohydrate Research Center, 315 Riverbend Road, The University of Georgia, Athens, Georgia 30602 USA (accessible on-line at http://glycoenzymes.ccrc.uga.edu/) have reported that expression constructs encoding all mammalian glycosylation enzymes has been generated, including glycosyltransferases, glycoside hydrolases, and glycan modifying enzymes. Many of the expression constructs express the glycosylation enzyme as a secreted soluble enzymes catalytic domains (when possible), including glycosylation enzymes with truncated transmembrane domains, replaced with signal sequences and fusion tags or other larger fusion proteins to facilitate detection, quantitation, and affinity purification, and includes expression vectors for production in mammalian cells, insect cells (baculovirus), and bacteria and protocols for protein production in each host system. The expression constructs are available from the DNASU Plasmid Repository located at DNASU/PSI: Biology-MR, Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287 USA (accessible on-line at https://dnasu.org/DNASU/Home.do)
The following examples are intended to promote a further understanding of the present invention.
Human serum IgG (14506), Tris-HCl (T-5941), HEPES (H4034), Sodium acetate (S2889), Calcium chloride (C5670), Magnesium chloride (M4880), Manganese Chloride solution (M1787), Sodium chloride solution (S5150), CMP-NANA (C8271), UDP-Gal (U4500), UDP-GlcNAc (U4375), GDP-Fuc (G4401), Acetonitrile (900667), Discovery glycan solid phase extraction (SPE) columns (55465-U), and empty SPE column and frit (57607-U) are purchased from Sigma-Aldrich. Protein A resin (53139), Protein A-IgG binding buffer (54200), Protein A-IgG elution buffer (21027), H2O (10977015) were purchased from ThermoFisher. Hydrophilic interaction liquid chromatography (HILIC) columns for chromatography (186004742), SPE uPlate (186002780), uPlate extraction manifold (186001831), SPE vacuum manifold (WAT200607), RapiGest SF (186008090), Glycoworks buffer (186008100), glycan quantitative standard (186008791), and Rapifluor-MS (186008091) were purchased from Waters. Molecular weight cutoff (MWCO) filters (UFC503096) were purchased from Millipore Sigma. Rapid PNGaseF (P0710) was purchased from NEB. Human FcR AlphaLISA Binding Kit (AL3081C) was purchased from Perkin Elmer.
Chromatography and mass spectrometry analyses were conducted using an Agilent 1290 Infinity II LC system tandem with Agilent 6500 Series quadrupole time-of-flight MS system. Enzyme concentration was determined by absorbance at 280 nm using NanoDrop 2000 (Thermo Scientific). Temperature-controlled reactions/incubations were performed in ThermoFisher MaxQ 6000 incubator and Fisherbrand Thermal Mizer II. Measurements of hydrodynamic diameter, melting temperature (Tm) and aggregation temperature (Tagg) were performed on Uncle (all-in-one biologics stability screening platform) from Unchained Labs. The detection of AlphaLISA-based assays for IgG-FcγR binding studies were conducted by EnVision Multimode Plate Reader 2105 (PerkinElmer). Refer to Tables 1A-C for the vendor information of glycosylation enzymes.
C. perfringens
A. ureafaciens
S. pneumoniae
S. pneumoniae
B. taurus (testis)
H. sapiens
3 ± 0.7
S. pneumoniae
S. picatus
B. Taurus (kidney)
C. Omnitrophica
Prunus dulcis
C. meningosepticum
E. miricola
H. sapiens
T. maritima
A. protophormia
S. pneumoniae
E. miricola
E. minicola
M. hiemalis
S. pyogenes
P. damsela
P. multocida
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
Homo sapiens
B. Taurus (milk)
H. sapiens
H. sapiens
6 ± 2.1
H. sapiens
(I) Resin loading: Empty SPE columns composed of an empty column body, a frit with 0.2 μm pores, and a lid were used as reaction vessels for SPGR reactions. The columns were mounted onto a 20-wells SPE vacuum manifold. 100 μL of protein A resin (wet resin) was transferred into each column, followed by conditioning with 0.8 mL protein A-IgG binding buffer twice. A vacuum system was connected to the manifold to control the flow rate.
(II) IgG immobilization: 1 mg (unless other specified) human serum IgG was added to 0.5 mL protein A-IgG binding buffer, followed by gently shaking until all the powder was dissolved. The solution was then transferred to the SPE column containing protein A resins. To ensure good immobilization, the columns were dismounted from the manifold, capped with Luer fittings, and then incubated for 15 minutes at room temperature with gentle rotating.
(III) Washing and conditioning: After the incubation, the columns were mounted to the manifold again, followed by washing with 0.8 mL protein A-IgG binding buffer (3 times) and then enzyme reaction buffer (2 times). After the conditioning step, the buffer was completely drained out from the columns.
(IV) Enzyme reactions: Enzyme reaction solutions were prepared by mixing the desired amount of enzyme, reaction buffer, and saccharide donors (1 mM, for glycosyltransferase) to a final volume of 100 μL unless other specified. Refer to Table 2 and Table 3 for the details of reaction conditions, including pH, concentration, and cation cofactors.
C. perfringens (nanH)
S. pneumoniae (bgaA)
S. pneumoniae (strH)
C. Omnitrophica
S. pyogenes (ndoS)
H. sapiens (ST6GAL1)
H. sapiens (B4GALT1)
H. sapiens (MGAT1)
H. sapiens (MGAT3)
H. sapiens (FUT8)
Genbank KXK31601.1
Enzyme reactions were initiated by transferring the reaction solution into SPE columns that contain immobilized IgG substrates. The columns were capped by Luer fitting, sealed with parafilm, and incubated at temperature-controlled shakers for a certain amount of time (Table 3). After the reaction, the enzyme solution was discarded (or recovered) and the 5 columns were washed 6-8 times with 0.8 mL protein A-IgG binding buffer via the extraction manifold.
3%
5%
1%
3%
3%
6%
2%
5%
3%
6%
(V) Elution of glycoengineered IgG: 500 μL protein A-IgG elution buffer was added to the reaction columns in two portions with a two-minute incubation for each at room temperature. The eluent was collected into a 0.5 mL MWCO (molecular weight cut-off) tube and concentrated via centrifugation at 14000 g for five minutes, followed by buffer exchange into 50 mM HEPES buffer (pH 8). After adjusting the concentration of the eluted IgG substrate to 3 mg/mL using NanoDrop, the IgG substrates were stored at 4° C. and were ready for analysis. IgG concentration was adjusted in this step in order to ensure the same amount of sample was charged to the downstream analyses.
This protocol is adapted from the Glycoworks manual provided by Waters.
(I) Glycan isolation: 7.5 μL IgG substrate (3 mg/mL, prepared as described above), 6 μL RapiGest SF (50 mg/ml, in Glycoworks buffer), and 15.3 μL water were mixed in a 1.5 mL microtube. The mixture was then incubated at 90° C. for five minutes to denature the substrates. After the samples were cooled down to room temperature, 1.2 μL Rapid PNGase F was added to the tube, followed by another incubation at 50° C. for 10 minutes.
(II) Glycan labeling: After PNGase F digestion, 12 μL RapiFluor-MS solution (70 mg/mL, in dimethylformamide (DMF)) was added to the solution. The mixture was gently vortexed and then incubated at room temperature for 20 minutes without any light exposure.
(III) Glycan purification: After labeling, the samples were diluted with 360 μL acetonitrile (1:9 volume ratio). Oasis SPE μPlate from Waters (along with the use of μPlate extraction manifold) was employed for the 1st solid-phase extraction purification, and Discovery SPE from Sigma-Aldrich (along with the use of 20-well SPE vacuum manifold) was used for the 2nd purification to ensure high signal-to-noise ratio: The SPE columns/μPlate were first washed by water (one column volume) and then conditioned by water-acetonitrile solution (10:90 v/v, one column volume). The glycan samples (in 90% acetonitrile solution) were then charged to the column/μPlate, followed by washing with washing buffer (formic acid/water/acetonitrile 1:9:90 v/v/v, two column volumes). The glycans were then eluted using 60 μL elution buffer (200 mM ammonium acetate in 5% acetonitrile).
(IV) HILIC-MS analysis: The purified glycan samples were injected to UPLC equipped with ACQUITY BEH Glycan column (130 Å, 1.7 μm, 2.1×150 mm) tandem with IMQ-TOF MS for glycan profile analysis. Refer to the literature published by Pucić et al. (Mol. Cell. Proteomics 10, M111.010090, doi: 10.1074/mcp.M111.010090 (2011)) and 1 Krištić et al. (J. Gerontol. A Biol. Sci. Med. Sci. 69, 779-789, doi: 10.1093/gerona/glt190 (2014)) for detailed peak assignment. The method provided by Waters for glycan chromatography used is shown in Table 4.
The conversion ratio of each SPGR reaction was calculated based on the consumption of the substrate glycan species. UV absorption at 260 nm (RapiFluor-MS) from chromatography analysis was used for the quantification of glycan populations. We first normalized the chromatographic peak area of the substrate glycan species to the total glycan peak area (Equation 1). This gives us the percentage of substrate glycan population. The reduction of the substrate glycan population after the reaction was then divided by the initial value to calculate the percentage of substrate conversion (Equation 2). We assume that there is no glycan shedding off from IgG during the experiments (namely, no endoglycosidase activity). Refer to Table 5 for detailed substrate species used in the calculation.
For endoglycosidase reactions, the activity was quantified by absolute glycan quantification using an internal standard. This is because endoglycosidases' activities result in the reduction of all glycan signals in the chromatography analyses. A known amount of internal standard (Glycan quantitative standard, Waters) was added to the sample to measure the amount of IgG glycan before and after the reactions.
CR50 is defined as the enzyme-to-substrate (IgG) molar ratio that leads to 50% substrate species conversion into the products in one hour at optimized working conditions (temperature, pH, cation) using SPGR. This value is determined based on dose-dependent experiments where the conversion ratio at different enzyme concentrations in one hour was tested. A sigmoidal curve fitting ([agonist] vs normalized response, GraphPad Prism, see the equation below) was then applied to the data for calculating the enzyme concentration that gives 50% substrate conversion. The resulting enzyme concentration is divided by the substrate (IgG) concentration to give CR50.
where Y is normalized response from 0 to 100; X is the concentration of enzyme.
Dynamic light scattering (DLS), melting temperature (Tm) and aggregation temperature (Tagg) studies were executed using UNcle (Unchainedlabs). Glycoengineered IgGs from SPGR reactions were eluted from protein A resins, followed by buffer exchange into HEPES buffer as described above. The protein concentration was then adjusted to 1 mg/ml using NanoDrop. Then, 9 μL of the purified IgG samples were injected into UNcle sample holders (five replicates for each sample). DLS measurement was performed at 25° C. (four acquisitions, five seconds each). Static light scattering (SLS) for Tm and Tagg measurement was carried out from 25° C. to 90° C. with a temperature increase of 0.3° C. per minute. All the tested IgG samples (1-10) contained an about 5% defucosylated population. The bi-antennary N-glycan samples (2-4) had about 10% bisecting glycoforms. The hybrid N-glycan samples (5-7) had about 10% (F)M3 glycans due to the reversible activity of GnT-I. Sialylated N-glycan samples (4 & 10) possessed about 1:1 mono- and bi-sialylated N-glycan populations. Refer to
This protocol is adapted from the AlphaLISA human FCGR binding kit manual provided by PerkinElmer. Briefly, serial dilutions of SPGR-engineered IgGs with 1× HiBlock buffer were prepared with the highest concentration at 1 mg/mL and the lowest concentration at 0.1 μg/mL. Then, 10 μL of each diluted IgG samples were mixed with 10 μL 4× human FcγRI solution and 20 μL Donor/acceptor beads solution into a white 96-well plate. The plate was then sealed and incubated at 25° C. for 90 minutes without any light exposure. After the reaction, the fluorescence signal at 615 nm was determined using an EnVision Multimode Plate Reader (equipped with AlphaScreen module).
Protein A homology model was constructed using the Swiss-Model server (Waterhouse et al., Nucleic Acids Res. 46, W296-w303, doi: 10.1093/nar/gky427 (2018)). PDB structure 5H7B, which has 79.5% sequence identity with Protein A, was used as a template to construct the homology model (Youn et al., Sci. Rep. 7, 2595, doi: 10.1038/s41598-017-02803-z (2017)). A visual inspection of Protein A model illustrated four distinct IgG binding domains. PDB structure 5U4Y was used as a template to identify the spatial positioning of the full-length Protein A and the IgG (Ultsch et al., Protein Eng. Des. Sel. 30, 619-625, doi: 10.1093/protein/gzx029 (2017)). The template structure contains only the B-domain of the protein A molecule. The spatial position of the B-domain helped us overlay the full-length protein-A molecule and allowed us to identify steric hindrances between other protein-A domains and the IgG molecule. Structure overlay and the movie illustrating clashes between the molecules was generated using Pymol (Molecular Graphics System, Version 2.0, Schrödinger LLC).
Data plotting and curve fitting were done by using GraphPad Prism 8. Figures and cartoons were created by Adobe Illustrator.
We use human IgG as the substrate in this study because it is a major class of glycoproteins that have been applied in therapeutic development (Kaplon & Reichert, MAbs 11:219-238, doi: 10.1080/19420862.2018.1556465 (2019); Lu et al., J. Biomed. Sci. 27: doi: 10.1186/s12929-019-0592-z (2020)). We quantitatively examined more than 30 glycan engineering enzymes for their activities on intact IgG immobilized on resins and then applied them in SPGR. This method has allowed us to harmonize IgG glycans into ten different glycoforms, including non-canonical structures, in 48 hours with an averaged conversion ratio greater than 95%. Physical and biochemical analyses indicated that the SPGR-engineered IgGs preserved integrity and functionality, suggesting that SPGR has high biocompatibility to the substrates.
Our strategy to achieve efficient, successive glycan remodeling is immobilizing IgG onto protein A resins and then executing enzymatic reactions heterogeneously (
To identify capable glycosylation enzymes for SPGR, we quantitatively analyzed the activity of 34 candidates, including exoglycosidases, endoglycosidases, and glycosyltransferases (
Trimming IgG Glycans with Glycosidases
IgGs have two highly conserved glycosylation sites on the crystallizable region (Fc) at Asn 297 where more than 20 complex-type glycoforms have been found with the majority in bi-antennary structures (
To control IgG glycoforms, we first aimed to harmonize them into the core saccharides by removing terminal sialic acid, galactose, and then GlcNAc. Neuraminidase (Neu, or sialidase) is a class of enzymes that cleaves the glycosidic linkages of sialic acids. Our screening showed that Neu from Clostridium perfringens has the highest activity on immobilized IgG with a CR50 of 1%. This enzyme has a broad substrate spectrum and can function on all the IgG glycoforms containing terminal sialic acid (
Fucose on IgG glycan chitobiose core has been known to modulate IgG binding affinity to Fc receptors (Ferrara et al., Proc Natl Acad Sci USA 108, 12669-12674, doi: 10.1073/pnas. 1108455108 (2011); et al., Genes Cells 16, 1071-1080, doi: 10.1111/j.1365-2443.2011.01552.x (2011)). Defucosylated IgG has been reported to have an over 50-fold increase in ADCC activity (Shields. et al., J Biol Chem 277, 26733-26740, doi: 10.1074/jbc.M202069200 (2002)). As such a strong regulator, controlling the level of IgG core fucose has become an attractive strategy for improving the efficacy of IgG-based drugs. Over 90% of the human serum IgG glycans are fucosylated (Pucić et al., Mol. Cell. Proteomics 10, M111.010090, doi: 10.1074/mcp.M111.010090 (2011)). To identify the enzymes that can trim fucose from intact IgGs in their native confirmations, we tested seven fucosidases (Fuc). Unfortunately, none of them showed an acceptable activity (Table 1). It has been reported that Fuc only functions on intact IgG when their glycans are trimmed down to the GlcNAc-fucose disaccharides, which indicates a strong steric interference between the Fuc-fucose interaction (Huang et al., J. Am. Chem. Soc. 134, 12308-12318, doi: 10.1021/ja3051266 (2012)). Inspired by works from Huang et al., we tested the Fuc panel with glycoengineered IgG bearing (F)M3 glycans, as prepared above. The enzyme from Candidatus omnitrophica showed significantly improved activity on this group of substrates (
Building IgG Glycans with Glycosyltransferases
Glycosyltransferases catalyze the transfer of saccharide(s) from activated sugar phosphates, the glycosyl donors, to glycosyl acceptor molecules, such as glycoproteins (Breton et al., Glycobiology 16, 29R-37R, doi: 10.1093/glycob/cwj016 (2005)). Sialyltransferase (SialyIT) from Homo sapiens exhibited the highest activity in our screening for installing sialic acid through α2-6 linkage to the IgG with terminal galactose. This enzyme has a relatively high CR so of 15.2% with an apparent substrate selectivity, as shown in
To install galactose on IgG glycans, we selected the galactosyltransferase (GalT) from Homo sapiens (
The addition of GlcNAc to the chitobiose core is relatively complicated because this process involves a series of N-Acetylglucosaminyltransferases (GnT) with various substrate specificities (
A higher level of bisecting GlcNAc on IgG results in enhanced ADCC activity and immune cells effector functions (Davies et al. Biotechnology and Bioengineering 74, 288-294, doi: 10.1002/bit.1119 (2001)). Reactions using serum IgG as the substrate suggested that human GnT-III can function on IgG glycoforms containing at least one terminal GlcNAc (
Tri- and tetra-antennary N-glycans are not typically reported on native human serum IgG, and were not observed in our studies. Human GnT-V (MGAT5) is reported to add the secondary GlcNAc to the α1-6 mannose through β1-6 linkage and leads to the formation of tri-/tetra-antennary glycoforms (Kim et al. Molec. Cell. Proteomics 7, 1-14, doi: 10.1074/mcp.M700084-MCP200 (2008); Shoreibah et al., J Biol Chem 268, 15381-15385 (1993)). We observed GnT-V activity after a 24-hours reaction with intact IgG, revealed by the formation of tri-antennary species. (
Finally, mammalian 1,6-fucosyltransferase (FucT) catalyzes the transfer of a fucose residue from GDP-fucose, the donor substrate, to the reducing-end terminal GlcNAc residue through an α1,6-linkage (Ihara et al., Glycobiology 16, 333-342, doi: 10.1093/glycob/cwj068 (2005)). The activity of FucT on intact IgG was observed but the conversion ratio was low, likely due to the strong steric hindrance on the substrate. We further boosted the FucT reaction by increasing both enzyme concentration and incubation time. The result indicated that FucT prefers IgGs bearing A2 and A2G1 glycoforms (
It was described how a Neu reaction followed by Gal treatment turned IgG glycans into GlcNAc-terminating glycoforms (
IgG bearing (F)M3 glycans can also serve as starting materials for rebuilding non-canonical glycoforms. Starting with the (F)M3 glycans, we applied GnT-I, GalT, and then SiaT reactions to construct a series of hybrid species (
To examine the biocompatibility of SPGR to the substrates, we analyzed the physical properties of the glycoengineered IgGs prepared above. Size analyses using dynamic light scattering (DLS) showed no significant difference between native serum IgG and SPGR-engineered IgGs, suggesting that there was no denaturing and/or aggregation occurred during the remodeling processes (
We reasoned these changes were attributed to the altered structure of IgG. It has been known that the Asn297 glycans play roles in maintaining the conformation and stability of the Fc region through intra-molecular interactions (Krapp et al., Journal of Molecular Biology 325, 979-989, doi: https://doi.org/10.1016/S0022-2836 (02) 01250-0 (2003); Fang et al., Biochemistry 55, 860-868, doi: 10.1021/acs.biochem.5b01323 (2016); Mimura et al., Mol Immunol 37, 697-706, doi: 10.1016/s0161-5890 (00) 00105-x (2000)). Decreased Tm and Tagg values were observed in IgGs terminating with mannose (Varki et al. in Essentials of Glycobiology, Cold Spring Harbor Laboratory Press, The Consortium of Glycobiology Editors, La Jolla, CA (2015)) or GlcNAc (Spiro, Glycobiology 12, 43R-56R, doi: 10.1093/glycob/12.4.43R (2002); Reily et al., Nature Reviews Nephrology 15, 346-366, doi: 10.1038/s41581-019-0129-4 (2019); van de Bovenkamp et al., Journal of Immunology 196, 1435-1441, doi: 10.4049/jimmunol. 1502136 (2016)), the glycoforms showing reduced intra-molecular interactions (Krapp et al., Journal of Molecular Biology 325, 979-989, doi: https://doi.org/10.1016/S0022-2836 (02) 01250-0 (2003)). Similarly, our hybrid glycans (5-7) had lower Tm values compared to others. These glycoforms lack the α1-6 arm which is important for forming intra-molecular interaction within the Fc region (Harbison et al., Glycobiology 29, 94-103, doi: 10.1093/glycob/cwy097 (2018). As expected, the removal of the bulk of the glycan structures using Endo S led to a dramatic drop in Tm and Tagg.
Next, we tested whether SPGR-engineered IgGs preserve the binding ability to FcRs. We performed a competition assay where the interaction between SPGR-engineered IgGs and Fc gamma receptor I (FcγR I) resulted in fluorescence signal reduction. A signal reduction of 60% was found in all the glycoengineered IgGs at the concentration of 0.1 μg/mL; while complete inhibitions were reached at about 10 μg/mL (
Beyond the presented work, there remains an opportunity to explore alternative immobilization strategies in future experiments. IgG immobilization using protein A, a 47 kD protein, likely limited the enzyme efficiency by creating a strong steric hindrance in some cases (Apweiler et al., Biochim Biophys Acta 1473, 4-8, doi: 10.1016/s0304-4165 (99) 00165-8 (1999)). Methods using oligopeptides, such as a HIS-tag, presumably have a lower steric effect and may enable higher enzyme activities. Since immobilization has been commonly employed for protein purification in pharmaceutical manufacturing processes, SPGR can conceivably be inserted into modern protein production processes as a “glycan modification module” to provide pure, glycoengineered proteins.
An alternative approach to conduct SPGR is immobilizing the glycosylation enzymes on solid supports instead of the IgG substrates (
Whether immobilization affects their activity and substrate selectivity, as well as the immobilization protocol itself, remains to be investigated.
IgG glycan trimming can also be implemented through the GlcNAc residues in the chitobiose core. Endoglycosidases specifically cleave the β1-4 linkage between the GlcNAc residues in the chitobiose core (Freeze et al., Curr. Protoc. Mol. Biol. Chapter 17, 10.1002/0471142727.mb0471141713as0471142789-0471142717.0471142713A, doi: 10.1002/0471142727.mb1713as89 (2010); Collin et al., EMBO J. 20, 3046-3055, doi: 10.1093/emboj/20.12.3046 (2001); Fan et al., Glycoconj J 13, 643-652, doi: 10.1007/bf00731453 (1996); Yamamoto et al., Biochem. Biophys. Res. Commun. 203, 244-252, doi: 10.1006/bbrc. 1994.2174 (1994)). They have been employed for chemoenzymatic glycan modification where the native glycans of targeted glycoprotein are first removed by endoglycosidases, followed by installing synthetic glycans back to the proteins using mutated endoglycosidases (glycosynthases) (Huang et al., J. Am. Chem. Soc. 134, 12308-12318, doi: 10.1021/ja3051266 (2012)). Since re-building the chitobiose cores remains challenging, largely due to the lack of available mannosyl-transferases, we analyzed the activity of endoglycosidases on intact IgG but did not apply them in SPGR applications. Of the six tested enzymes, the candidate from Streptococcus pyogenes (known as Endo S) exhibited the highest conversion ratio on intact IgG (CR50=0.7%,
With the use of high enzyme concentration and long incubation time, we found that Fuc from C. omnitrophica functioned on all the IgG glycoforms. (
IgG immobilization enables efficient washing and reaction-swapping processes in SPGR. However, we observed reduced enzyme activities on immobilized IgG compared to non-immobilized, free IgG (
While the present invention is described herein with reference to illustrated embodiments, it should be understood that the invention is not limited hereto. Those having ordinary skill in the art and access to the teachings herein will recognize additional modifications and embodiments within the scope thereof. Therefore, the present invention is limited only by the claims attached herein.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2022/024194 | 4/11/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63175602 | Apr 2021 | US |
