WO2017156192A1 - Methods for modular synthesis of n-glycans and arrays thereof - Google Patents

Methods for modular synthesis of n-glycans and arrays thereof Download PDF

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Publication number
WO2017156192A1
WO2017156192A1 PCT/US2017/021454 US2017021454W WO2017156192A1 WO 2017156192 A1 WO2017156192 A1 WO 2017156192A1 US 2017021454 W US2017021454 W US 2017021454W WO 2017156192 A1 WO2017156192 A1 WO 2017156192A1
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glycans
present disclosure
glycan
benzyl
group
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PCT/US2017/021454
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French (fr)
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Chi-Huey Wong
Chung-Yi Wu
Sachin S. Shivatare
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Academia Sinica
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Priority to JP2018547330A priority Critical patent/JP2019515876A/en
Priority to AU2017231749A priority patent/AU2017231749A1/en
Priority to EP17764050.5A priority patent/EP3426693A4/en
Priority to KR1020187028421A priority patent/KR20180114210A/en
Priority to CA3016170A priority patent/CA3016170A1/en
Priority to CN201780027439.5A priority patent/CN109195996A/en
Publication of WO2017156192A1 publication Critical patent/WO2017156192A1/en
Priority to IL261517A priority patent/IL261517A/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H5/00—Compounds containing saccharide radicals in which the hetero bonds to oxygen have been replaced by the same number of hetero bonds to halogen, nitrogen, sulfur, selenium, or tellurium
    • C07H5/04—Compounds containing saccharide radicals in which the hetero bonds to oxygen have been replaced by the same number of hetero bonds to halogen, nitrogen, sulfur, selenium, or tellurium to nitrogen
    • C07H5/06—Aminosugars
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    • C08B—POLYSACCHARIDES; DERIVATIVES THEREOF
    • C08B37/00—Preparation of polysaccharides not provided for in groups C08B1/00 - C08B35/00; Derivatives thereof
    • C08B37/006—Heteroglycans, i.e. polysaccharides having more than one sugar residue in the main chain in either alternating or less regular sequence; Gellans; Succinoglycans; Arabinogalactans; Tragacanth or gum tragacanth or traganth from Astragalus; Gum Karaya from Sterculia urens; Gum Ghatti from Anogeissus latifolia; Derivatives thereof
    • C08B37/0063—Glycosaminoglycans or mucopolysaccharides, e.g. keratan sulfate; Derivatives thereof, e.g. fucoidan
    • C08B37/0075—Heparin; Heparan sulfate; Derivatives thereof, e.g. heparosan; Purification or extraction methods thereof
    • C08B37/0081—Reaction with amino acids, peptides, or proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
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    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
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    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
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    • C08B37/00—Preparation of polysaccharides not provided for in groups C08B1/00 - C08B35/00; Derivatives thereof
    • C08B37/006—Heteroglycans, i.e. polysaccharides having more than one sugar residue in the main chain in either alternating or less regular sequence; Gellans; Succinoglycans; Arabinogalactans; Tragacanth or gum tragacanth or traganth from Astragalus; Gum Karaya from Sterculia urens; Gum Ghatti from Anogeissus latifolia; Derivatives thereof
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1048—Glycosyltransferases (2.4)
    • C12N9/1051—Hexosyltransferases (2.4.1)
    • C12N9/107—1,4-Alpha-glucan branching enzyme (2.4.1.18)
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    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/04—Polysaccharides, i.e. compounds containing more than five saccharide radicals attached to each other by glycosidic bonds
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    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
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    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • G—PHYSICS
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    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56983—Viruses
    • G01N33/56988—HIV or HTLV
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
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    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
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    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16061—Methods of inactivation or attenuation
    • C12N2740/16063—Methods of inactivation or attenuation by chemical treatment
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
    • Y02P20/00—Technologies relating to chemical industry
    • Y02P20/50—Improvements relating to the production of bulk chemicals
    • Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Definitions

  • the present disclosure is related generally to chemical and chemo-enzymatic methods for synthesis of highly diverse N-glycans of high mannose, hybrid and complex types, arrays made from said glycans, and use of said arrays.
  • the present disclosure relates to methods of synthesis of N-glycan arrays on aluminum oxide coated substrate using a novel modular N-glycans synthetic approach, and the use of said N-glycan arrays for detection and analysis of binding reactions by glycan-binding molecules such as broadly neutralizing HIV antibodies.
  • N-linked glycosylation of proteins is a fundamental and important post-translational modification found both in eukaryotes and in prokaryotes. This protein modification results in the covalent attachment of an oligosaccharide onto asparagine residues of polypeptide chains.
  • Glycans are typically the most important interface between cells and their environment. As a vital constituent of all living systems, glycans are involved in most of the essential biological processes such as protein folding, cell signaling, fertilization, embryogenesis, and the proliferation of cells and their organization into specific tissues.
  • Abnormal cell surface glycosylation and/or glycan-profiles are usually related to diseases such as cancer and atherosclerosis. Accordingly, altered glycosylation is an indication of an early and possibly critical point in development of human pathologies. Thus, insights into the carbohydrate related biological and pathological processes, and for developing diagnostics and therapeutics for human diseases.
  • glycan building blocks monosaccharides
  • These cell-identifying glycosylated molecules include glycoproteins and glycolipids and are specifically recognized by various glycan binding molecules such as lectins, antiglycan antibodies, chemical compounds and also other glycans and glycolipids, etc.
  • glycan binding molecules such as lectins, antiglycan antibodies, chemical compounds and also other glycans and glycolipids, etc.
  • nucleotide and protein microarrays have revolutionized genomic, gene expression and proteomic research.
  • development of glycan microarrays has allowed an unprecedented high-throughput exploration of the specificities of a diverse range of glycan-binding molecules.
  • the systematic arrangement of glycans on arrays allow for efficient probing of low affinity protein-glycan interactions through multivalent presentation. Since their establishment, various types of “arrays” have been developed, including the one available from the Consortium of Functional Glycomics (CFG) which contains more than 600 oligosaccharides on an N-hydroxysuccinimide (NHS)-activated glass slide.
  • CFG Functional Glycomics
  • the final oligosaccharide products are equipped with amino alkyl linker at the reducing end to restore its structural integrity and to act as handle for immobilization on arrays, or in certain other embodiments, said products can alternatively be conjugated to carrier proteins.
  • a preferred orthogonally protected Man ⁇ 1–4GlcNAc ⁇ 1–4GlcNAc ⁇ 1 core trisaccharide contains at least two ortho onal rotectin rou s, and has the formula (I) Wherein each of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 is independently selected from the group consisting of an orthogonal or a permanent protecting group; wherein, each of the orthogonal protecting group at R 6 is preferably selected from para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), levulinoyl (Lev), benzoyl (Bz), allyl ether (Allyl), and silyl ethers; and R 7 and R 8 are fused to form benzylidene ring which can be cleaved to form either 4-OH and/or 6-OH;
  • PMB para-methoxy benzyl ether
  • PMP me
  • Each of R 2 , R 3 , R 4 , and R 5 is independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac);
  • R 1 is a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac); or a protected fucoside residue connected via ⁇ 1,6 linkage;
  • X is–OR 9 ; wherein R 9 is–H or optionally substituted C3-C10 alkyls chain terminated with groups consisting of–N3 or NR 10 ; and R 10 is–H or benzyl (Bn) or carbobenzoyl (Cbz);
  • R 11 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) or tert-butoxycarbonyl (Boc).
  • a“permanent protecting group” can be a chemical moiety that prevents functionalization of a functional group when exposed to conditions which would normally functionalize said functional group.
  • the permanent protecting group can be selectively removed to expose the functional group in the resulting molecule.
  • the exposed functional group can be further reacted with another moiety, or can be left unfunctionalized.
  • the preferred D1 and D2/D3 arm modules has the general formula (II)
  • each of R 1 , R 2 , R 3 , and R 4 is–H or a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
  • Each of R 5 , R 6 , R 7 , and R 8 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz);
  • Each of R 9 and R 10 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or a protected fucoside residue connected via ⁇ 1,3 linkage to GlcNAc and/or ⁇ 1,2 linkage to Galactose;
  • R 11 is–H or Me, Et
  • R 13 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
  • X is–OR 14 or–SR 15
  • R 14 is H, alkyl, alkenyl, alkynyl, aryl or substituted aryl; a protecting group such as a silyl or substituted silyl, preferably thexyldimethylsilyl (TDS), t-butyldimethylsilyl (TBS), t- butyldiphenyl silyl (TBDPS), triisopropylsilyl (TIPS), trimethylsilyl (TMS), or triethylsilyl (TES); methyl (Me), acetyl (Ac), benzyl (Bn), 2-naphthylmethyl (Nap) or 1- naphthylmethyl (1-Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), allyl ether (Allyl), or an anomeric leaving group such as fluoride–F, trichloroacetimidate - C(NH)-(NH
  • R 15 is H, alkyl, aryl, or substituted aryl, preferably methyl, ethyl, phenyl, tosyl, or tolyl.
  • the D1 and D2/D3 arm modules of general formula (II) are prepared chemically or preferably chemo-enzymatically.
  • the examplars of chemically s nthesized D1 and D2/D3 arm modules are selected from the rou consistin of
  • each of R 1 and R 2 is independently selected from–H or the protecting groups acetyl (Ac) or benzoyl (Bz);
  • X is–OR 3 and R 3 is H, benzyl (Bn), 2-naphthylmethyl (Nap) or 1-naphthylmethyl (1- Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), allyl ether (Allyl).
  • the chemo-enzymatically prepared acceptor substrates of formula (III) are subjected to enzymatic extensions, wherein the enzymes are independently selected from the group consisting of ⁇ (1 ⁇ 4)
  • Galactosyltransferase ⁇ (1 ⁇ 3) Fucosyltransferase, ⁇ (1 ⁇ 2) Fucosyltransferase, ⁇ (1 ⁇ 3) N- acetyl glucosamine transferase, ⁇ (2 ⁇ 3) sialyltransferase, and ⁇ (2 ⁇ 6) sialyltransferase.
  • the chemo-enzymatically prepared modules of formula (II) can be transformed into their acetates or benzoates form.
  • the fully acetylated or benzoylated modules of formula (II) can undergo reducing end modification to form an anomeric leaving group such as trichloroacetimidate -C(NH)-CCl 3 , phenyltrifluoroacetimidate -C(NPh)-CF 3 ,
  • D1 and D2/D3 arm modules of formula (II) are independently selected for chemical glycosylation at 3-O and/or 6-O positions of Man ⁇ 1–4GlcNAc ⁇ 1–4GlcNAc ⁇ 1 core trisaccharide of formula (I).
  • the present disclosure also provides an orthogonally protected Man ⁇ 1–4GlcNAc ⁇ 1 core containing at least two orthogonal protecting groups, and has the formula (IV) Wherein each of R 1 , R 2 , R 3 , R 4 , R 5 , and R 6 is independently selected from the group consisting of an orthogonal or a permanent protecting groups; wherein, each of the orthogonal protecting groups at R 4 is preferably selected from para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), levulinoyl (Lev), benzoyl (Bz), allyl ether (Allyl), and silyl ethers; and R 5 and R 6 are fused to form benzylidene ring which can be cleaved to form either 4-OH and/or 6-OH;
  • PMB para-methoxy benzyl ether
  • PMP methoxy phenyl ether
  • Lev levulinoyl
  • Bz benzoy
  • Each of R 1 , R 2 , and R 3 is independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac);
  • X is–OR 7 ; wherein R 7 is–H or benzyl (Bn) or allyl (All);
  • Y is–NHR 8 ; and R 8 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) or tert-butoxycarbonyl (Boc).
  • Fmoc 9- fluorenylmethoxycarbonyl
  • Alloc allyloxycarbonyl
  • Troc [2,2,2- Trichloroethoxycarbonyl]
  • acetyl Ac
  • Phth phthalimido
  • Cbz carbobenzyloxy
  • Boc tert-butoxycarbonyl
  • conditions effective to cause cleavage of each of the different orthogonal protecting groups preferably do not cause cleavage of other protecting groups present on the oligosaccharide building blocks.
  • the N-glycan core structure is optionally equipped with a spacer or linker and includes - (CH 2 ) 5 NH 2 at the reducing end to facilitate efficient immobilization on arrays and conjugation to carrier proteins.
  • the present disclosure also provides spacers such as -(CH2) nNH-CO-O-[(CH2)2-O-(CH2)2]2-3-O-PO(OH)2 to facilitate efficient immobilization on aluminum oxide arrays through phosphonate chemistry.
  • the present disclosure provides a method for making an orthogonally protected Man ⁇ 1–4GlcNAc ⁇ 1-4GlcNAc ⁇ 1 core.
  • the present disclosure provides chemical and chemo-enzymatic methods for making D1 and D2/D3 arm modules.
  • the present disclosure provides the strategy to prepare thousands of structurally-distinct complex N-linked oligosaccharides (N-glycans), wherein the material can be used for (1) development of glycan arrays to determine binding specificities of carbohydrate binding molecules such as lectins, galactose binding proteins (galectins), anti- glycan antibodies, HIV broadly neutralizing antibodies, and preferably of influenza hemagglutinin, chemical compounds and also other glycans and glycolipids; (2) standards for glycan sequencing using mass spectrometry; (3) preparation of diverse glycoforms at Fc- region of therapeutic antibodies such as Rituxan, Herceptin, Humira for enhancement of their effector functions; and (4) oligosaccharides standards for glycobiology research laboratories.
  • N-glycans N-linked oligosaccharides
  • the present disclosure comprises an array of carbohydrate moieties immobilized on a substrate, the array comprising: a plurality of glycans wherein one or more glycan moieties are deposited at a discrete location (e.g. a spot) on the substrate, wherein the diverse glycans comprises homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types wherein the array is useful for the detection of hetero-glycan binding behavior.
  • the present disclosure comprises a method for detecting hetero-glycan binding behavior comprising contacting the array with one or a plurality of hetero-glycans.
  • the hetero-glycans can be part of broadly neutralizing HIV-1 antibodies.
  • the glycans comprising homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types are prepared by modular chemo-enzymatic methods.
  • the use of an array for the detection of hetero-glycan binding behavior comprises the steps of detecting binding specificity of broadly neutralizing HIV-1 antibodies.
  • the glycans comprises one or more of the compounds G1- G33 as set forth in Figure S11 and/or any one or more of the compounds I-XI as set forth in Figure S17.
  • the glycans can include or exclude one or more of the compounds G1-G33 as set forth in Figure S11 and includes or excludes any one or more of the compounds I-XI as set forth in Figure S17.
  • a method for generating vaccine targets comprising screening and identification of optimal cell surface glycans recognized by neutralizing HIV-1 antibodies, wherein the method further comprises contacting the HIV antibodies with the array of any one of claims 1-6, is provided.
  • a glycan microarray on an aluminium oxide-coated glass (ACG) slide, or an indium tin-oxide-coated (ITO) glass slide, containing a diverse set of glycans, including homo- and mixed N-glycans of high-mannose-, hybrid-, and complex- type prepared by modular chemo-enzymatic methods is provided.
  • the array is useful for the detection of hetero-glycan binding behaviors.
  • the method of generating/fabricating said glycan microarray is provided.
  • synthetic strategy based on diversity can be created by assembly of the so called “D1 and D2/D3 arm modules", followed by the ⁇ -specific mannosylation at the 3-O and/or 6-O position of the mannose residue of the common core trisaccharide.
  • the glycosyl fluoride strategy was combined with enzymatic sialylation to build a library of symmetric bi-, tri- and tetraantennary complex-type glycans 50.
  • modular synthetic methods for preparation of high mannose, hybrid and asymmetrically sialylated multi-antennary glycans are provided (e.g. Fig.1b).
  • a method for rapid screening and identification of optimal glycans recognized by neutralizing antibodies is provided.
  • the screening directly facilitates development of HIV-1 vaccines targeting cell surface glycans.
  • this disclosure relates to screening libraries of glycan binding partners to identify N-glycan binding partners that bind to an array comprising one or more N-glycans as disclosed herein.
  • the molecules in said libraries may comprise, for example, antibodies, nanobodies, antibody fragments, aptamers, lectins, peptides, biomolecules, or combinatorial library molecules.
  • said screening comprises a detection step, wherein the detection step comprises the detection of N-glycan binding by a HIV antibody.
  • the detection of said HIV antibody comprises the use of a N-glycan array, comprising one or more N-glycans as disclosed herein.
  • this disclosure relates to a method of of detecting N-glycan binding wherein a complex is formed by contacting the array with one or a plurality of N-glycans, and contacting the complex with a label.
  • the label can then be detected.
  • the label can be a labeled antibody.
  • the labeled antibody can further comprise a label comprising an enzyme, fluorophore, a chemiluminescent moiety, or a nanoparticle.
  • this disclosure relates to a method of detecting HIV antibodies, the method comprising: providing an array of N-linked glycans as described herein, contacting the array with HIV antibodies; forming a complex between the HIV antibodies and the glycans on the array; contacting the HIV antibody-glycan array complex with a label; and detecting the label.
  • the label can be a labeled antibody further comprising an enzyme, fluorophore, chemiluminescent moiety, or a nanoparticle.
  • the interaction between A and X can, in some embodiments, be a covalent bond, Van der Waals interaction, hydrogen bond, ionic bond, or hydrophobic interaction.
  • FIG. 1 shows an exemplary general strategy for the modular synthesis of N-glycans. Due to the large number of possible glycosidic linkages and the generation of a diversity of structures, especially from the GlcNAc residues to the non-reducing end, a modular approach is used to minimize the reaction steps and create enough diversity to reflect the nature of N-glycosylation.
  • FIG. 1A The synthesis of high mannose-, hybrid-, and complex-type N-glycans through the regio- and stereoselective glycosidation of orthogonally protected core trisaccharide at the 3-O and 6-O positions with a modular set of diverse glycosyl donors.
  • FIG.1B The representative N-glycans that can be generated by this strategy
  • FIG.1C Retrosynthetic disconnections of high-mannose-, hybrid- and complex-type glycans showing the required building blocks for assembly.
  • Figure 2 shows exemplary structures of D1 and D2/D3 arm building blocks.
  • a modular set of building blocks that are prepared by total chemical synthesis and used for oligosaccharide assembly.
  • FIG.3 shows exemplary chemo-enzymatic synthesis of modules.
  • Reagents and conditions i), UDP-galactose, ⁇ -1, 4-GalT; ii), GDP-fucose, ⁇ -1, 3-FucT; iii), CMP-Neu5Ac, ⁇ -2, 6-SiaT; iv), CMP-Neu5Ac, ⁇ -2, 3-SiaT; v), GDP-fucose, ⁇ -1, 2-FucT; vi), NaOH.
  • Figure 4 is a representative proof-of-concept demonstration of chemo-enzymatic strategy to N-glycan synthesis.
  • Reagents and conditions i), acetic anhydride, pyridine; ii), (1) CAN, toluene: ACN: H 2 O: toluene; (2) DAST, CH 2 Cl 2 , -30 o C; iii), AgOTf, Cp 2 HfCl 2 , toluene, 4 ⁇ MS, 0 o C to rt; iv), p-TSA, acetonitrile, rt; v), (1) LiOH, 1,4-dioxane: H2O; 90 o C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH) 2 , MeOH: H 2 O: HCOOH (5: 3: 2), H 2 .
  • CAN Cerium ammonium nitrate
  • DAST Die
  • Cp2HfCl2 Bis(cyclopentadienyl)hafnium dichloride
  • MS molecular sieves.
  • FIG 5 shows exemplary glycan specificities of HIV-1 bNAbs on ACG array.
  • FIG 5A. Synthetic N-glycans are chemically modified with a phosphonic acid tail for covalent attachment to the aluminium oxide-coated glass (ACG) slide through phosphonate chemistry.
  • FIG.5B FIG.5C
  • FIG.5D Binding of PG9, PG16 and PGTs 141-144 to structures I-XI printed on an ACG slide
  • FIG.5E Binding of PG9 and PG16 to each of the glycan mixtures was evaluated to determine the effect of adjacent glycans on binding affinity.
  • Arrays were printed by mixing 100 ⁇ M of
  • the molar concentrations in ⁇ M for antibodies are given in the legend.
  • the mean signal intensities and standard error calculated for five independent replicates on the array are shown.
  • Figures 6A and 6B shows exemplary glycan specificities of PG9 (panel A– FIG.6A) and PG16 (panel B– FIG.6B) to mixture of Man5 and XI at various ratios.
  • Arrays were printed by 100 ⁇ M of linker, Man 5 GlcNAc 2 (IV), complex type glycan (XI) and each of the mixtures of (IV + XI) or (XI + IV) in a 1:1/2/3/4/5 ratio.
  • the molar concentrations in ⁇ M for antibodies are given in the legend.
  • the mean signal intensities and standard error calculated for eight independent replicates on the array are shown.
  • Figure 7 shows an exemplary structure embodiments of the present disclosure.
  • Figure 8 shows an exemplary structure embodiments of the present disclosure.
  • Figure 9 shows an exemplary structure embodiments of the present disclosure.
  • Figure 10 shows an exemplary structure embodiments of the present disclosure.
  • FIG.11A shows an exemplary structure embodiments of the present disclosure.
  • FIG.11B shows an exemplary structure embodiments of the present disclosure.
  • FIG.11C shows an exemplary structure embodiments of the present disclosure.
  • Figure 12 shows an exemplary structure embodiments of the present disclosure.
  • Figure 13 shows an exemplary structure embodiments of the present disclosure.
  • Figure 14 Exemplary Modular synthesis of high mannose, hybrid- and complex-type N-glycans.
  • FIG.15A to 15C Exemplary sugar residues of representative highmannose, hybrid and complex type oligosaccharides.
  • FIG.15A High Mannose type
  • FIG.15B hybrid type
  • FIG. 15C complex type).
  • Figure 16 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 17 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 18 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 19 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 20 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 21 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 22 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 23 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 24 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 25 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 26 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 27 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 28 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 29 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 30 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 31 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.32A shows exemplary structure embodiments in a representative synthetic scheme embodiments of the present disclosure.
  • FIG.32B shows exemplary structure embodiments in a representative synthetic scheme embodiments of the present disclosure.
  • FIG.32C shows exemplary structure embodiments in a representative synthetic scheme
  • Figure 33 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 34 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 35 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 36 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.37A shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.37B shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.37C shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 38 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 39 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 40 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 41 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.42A shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
  • FIG.42B shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
  • Figure 43 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 44 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 45 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 46 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.47A shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
  • FIG.47B shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
  • FIG.47C shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
  • Figure 48 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 49 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 50 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 51 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 52 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 53 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 54 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 55 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 56 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 57 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 58 Exemplary Structures of high mannose type glycans and their fragments.
  • FIG.59A and 59B FIG.59A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.59B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.60A Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.60B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 61 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 62 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 63 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 64 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 65 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 66 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 67 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 68 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 69 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 70 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 71 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 72 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 73 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 74 Exemplary Structures of hybrid type glycans and their fragments.
  • FIG.75A Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.75B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 76 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 77 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 78 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 79 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 80 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 81 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.82A Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.82B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.82C Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.82D Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 83 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 84 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 85 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 86 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 87 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.89A and 89B FIG.89A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.89B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 90 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 91 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 92 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.93A Exemplary Structures of complex type glycans.
  • FIG.93B Exemplary Structures of complex type glycans.
  • FIG.93C Exemplary Structures of complex type glycans.
  • Figure 94 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 95 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 96 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 97 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 98 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 100 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 101 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.102A and 102B FIG.102A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.102B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 103 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 104 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 105 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 106 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 107 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 108 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 109 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 111 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 112 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 114 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 115 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 116 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 117 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG.118A, 118B, and 118C FIG.118AExemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.118B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG.118C Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 119 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 120 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 121 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 122 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 123 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 124 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 125 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 126 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 127 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 128 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 129 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 130 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 131 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 132 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 134 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 135 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 136 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 137 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 139 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 140 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 141 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 142 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 143 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 144 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 145 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 146 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 148 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 149 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 150 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 151 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 154 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 155 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 156 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 157 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 158 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 159 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 161 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 162 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 163 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 164 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 165 Scheme S25 Exemplary Preparation scheme of assymetric module.
  • Figure 166 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 167 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 168 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 169 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 170 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 171 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 172 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 173 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 174 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 175 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 176 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 177 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 178 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 179 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 180 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 181 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 182 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • FIG. 183A and 183B FIG. 183A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • FIG. 183B Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
  • Figure 184 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 185 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 186 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 187 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 188 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 189 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 190 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
  • Figure 191 Figure S4 Schematic drawing of the fabrication of anodized aluminum oxide (AAO) glass substrate.
  • AAO anodized aluminum oxide
  • FIG. 192A AFM picture– Roughness Analysis of the surface. Img. Rms (Rq) 2.319 nm and FIG. 192B) Cross Section SEM picture of the AAO Glass Substrate.
  • Figure 193 Figure S6 Structures of Cy5-phosphonic acid linker and Cy5-amine linker.
  • Figure 194 Figure S8 Representative Confocal Microscopes pictures Cy5- phosphonic Acid, and Cy5-Amine on AAO glass substrate and NHS glass slide. Selective 900 ⁇ m2 area within the spots
  • Figure 195A, 195B, and 195C Figure S7
  • Figure 196 Figure S9
  • FIG. 197A and 197B Figure S10
  • Figure 198 Figure S11 Schematic representation of N-glycans printed on NHS coated glass slide.
  • Figure 199 Figure S12. Binding behavior of PG16 using NHS-coated glass slide. Bindings of PG16 to panel of N-glycans represented in bar chart.
  • Figure 200 Figure S17. Cartoon represents glycans printed on ACG array. The structure of linker is shown on the upper left corner.
  • Figure 201A and 201B Figure S18). Bindings of PGTs 141-144 towards panel of N-glycans on ACG array is shown in bar chart.
  • Figure 202A and 202B Figure S19). Antibody PG16 binding curves observed for glycans X, XI and mixtures V+XI and X+XII at 100 ⁇ M concentration. The curves were obtained by using DyLight649-conjugated donkey anti-Human IgG secondary antibody.
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al.,
  • C1–6 is intended to encompass C1, C2, C3, C4, C5, C6, C1–6, C1–5, C1–4, C1–3, C1–2, C2–6, C2–5, C2–4, C2–3, C3–6, C3–5, C3–4, C4–6, C4–5, and C5–6.
  • Alkyl refers to a radical of a straight–chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C1–20 alkyl”). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C 1–10 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C1–9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1–8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C1–7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C 1–6 alkyl”).
  • an alkyl group has 1 to 5 carbon atoms (“C1–5 alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C 1–4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C1–3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C1–2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C 2–6 alkyl”).
  • C1–6 alkyl groups include methyl (C1), ethyl (C2), n-propyl (C3), iso-propyl (C3), n-butyl (C 4 ), tert-butyl (C 4 ), sec-butyl (C 4 ), iso-butyl (C 4 ), n-pentyl (C 5 ), 3–pentanyl (C 5 ), amyl (C5), neopentyl (C5), 3–methyl–2–butanyl (C5), tertiary amyl (C5), and n-hexyl (C6).
  • alkyl groups include n-heptyl (C7), n-octyl (C8) and the like. Unless otherwise specified, each instance of an alkyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkyl”) or substituted (a“substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is unsubstituted C 1–10 alkyl (e.g.,– CH3). In certain embodiments, the alkyl group is substituted C1–10 alkyl.
  • alkenyl refers to a radical of a straight–chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon–carbon double bonds, and no triple bonds (“C2–20 alkenyl”).
  • an alkenyl group has 2 to 10 carbon atoms (“C 2–10 alkenyl”).
  • an alkenyl group has 2 to 9 carbon atoms (“C 2–9 alkenyl”).
  • an alkenyl group has 2 to 8 carbon atoms (“C 2–8 alkenyl”).
  • an alkenyl group has 2 to 7 carbon atoms (“C2–7 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C2–6 alkenyl”).
  • an alkenyl group has 2 to 5 carbon atoms (“C 2–5 alkenyl”). In some
  • an alkenyl group has 2 to 4 carbon atoms (“C2–4 alkenyl”). In some
  • an alkenyl group has 2 to 3 carbon atoms (“C 2–3 alkenyl”). In some
  • an alkenyl group has 2 carbon atoms (“C2 alkenyl”).
  • the one or more carbon– carbon double bonds can be internal (such as in 2–butenyl) or terminal (such as in 1–butenyl).
  • Examples of C 2–4 alkenyl groups include ethenyl (C 2 ), 1–propenyl (C 3 ), 2–propenyl (C 3 ), 1– butenyl (C4), 2–butenyl (C4), butadienyl (C4), and the like.
  • C2–6 alkenyl groups include the aforementioned C 2–4 alkenyl groups as well as pentenyl (C 5 ), pentadienyl (C 5 ), hexenyl (C6), and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (C8), octatrienyl (C8), and the like. Unless otherwise specified, each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certain embodiment of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certain
  • the alkenyl group is unsubstituted C 2–10 alkenyl. In certain embodiments, the alkenyl group is substituted C2–10 alkenyl.
  • an alkynyl group has 2 to 7 carbon atoms (“C2–7 alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C 2–6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C2–5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C 2–4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C 2–3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C2 alkynyl”).
  • the one or more carbon– carbon triple bonds can be internal (such as in 2–butynyl) or terminal (such as in 1–butynyl).
  • Examples of C 2–4 alkynyl groups include, without limitation, ethynyl (C 2 ), 1–propynyl (C 3 ), 2–propynyl (C3), 1–butynyl (C4), 2–butynyl (C4), and the like.
  • Examples of C2–6 alkenyl groups include the aforementioned C 2–4 alkynyl groups as well as pentynyl (C 5 ), hexynyl (C6), and the like.
  • alkynyl examples include heptynyl (C7), octynyl (C8), and the like. Unless otherwise specified, each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is unsubstituted C 2–10 alkynyl. In certain embodiments, the alkynyl group is substituted C2–10 alkynyl.
  • Carbocyclyl or“carbocyclic” refers to a radical of a non–aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C 3–10 carbocyclyl”) and zero heteroatoms in the non–aromatic ring system.
  • a carbocyclyl group has 3 to 8 ring carbon atoms (“C 3–8 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C3–6 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C3–6 carbocyclyl”).
  • a carbocyclyl group has 5 to 10 ring carbon atoms (“C 5–10 carbocyclyl”).
  • Exemplary C 3–6 carbocyclyl groups include, without limitation, cyclopropyl (C3), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C 5 ), cyclopentenyl (C 5 ), cyclohexyl (C 6 ), cyclohexenyl (C 6 ), cyclohexadienyl (C6), and the like.
  • Exemplary C3–8 carbocyclyl groups include, without limitation, the aforementioned C3–6 carbocyclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C 7 ), cycloheptatrienyl (C 7 ), cyclooctyl (C 8 ), cyclooctenyl (C 8 ), ydroxy[2.2.1]heptanyl (C7), ydroxy[2.2.2]octanyl (C8), and the like.
  • Exemplary C3–10 carbocyclyl groups include, without limitation, the aforementioned C 3–8 carbocyclyl groups as well as cyclononyl (C 9 ), cyclononenyl (C 9 ), cyclodecyl (C 10 ), cyclodecenyl (C 10 ), octahydro–1H–indenyl (C9), decahydronaphthalenyl (C10), spiro[4.5]decanyl (C10), and the like.
  • the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated.
  • “Carbocyclyl” also includes ring systems wherein the carbocyclic ring, as defined above, is fused to one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclic ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system.
  • each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted carbocyclyl”) or substituted (a“substituted carbocyclyl”) with one or more substituents.
  • the carbocyclyl group is unsubstituted C3–10 carbocyclyl.
  • the carbocyclyl group is a substituted C3–10 carbocyclyl.
  • “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C 3–10 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C3–8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C3–6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C 5–6 cycloalkyl”).
  • a cycloalkyl group has 5 to 10 ring carbon atoms (“C5–10 cycloalkyl”).
  • C5–6 cycloalkyl groups include cyclopentyl (C 5 ) and cyclohexyl (C 5 ).
  • C 3–6 cycloalkyl groups include the aforementioned C5–6 cycloalkyl groups as well as cyclopropyl (C3) and cyclobutyl (C4).
  • Examples of C3–8 cycloalkyl groups include the aforementioned C3–6 cycloalkyl groups as well as cycloheptyl (C 7 ) and cyclooctyl (C 8 ).
  • each instance of a cycloalkyl group is independently unsubstituted (an“unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents.
  • the cycloalkyl group is unsubstituted C 3–10 cycloalkyl. In certain embodiments, the cycloalkyl group is substituted C3–10 cycloalkyl.
  • Heterocyclyl or“heterocyclic” refers to a radical of a 3– to 10–membered non– aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3–10 membered heterocyclyl”).
  • the heteroatom is independently selected from nitrogen, sulfur, and oxygen.
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or partially unsaturated.
  • Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system.
  • each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an“unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents.
  • the heterocyclyl group is unsubstituted 3–10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3–10 membered heterocyclyl.
  • a heterocyclyl group is a 5–10 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5–10 membered heterocyclyl”).
  • a heterocyclyl group is a 5–8 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–8 membered heterocyclyl”).
  • a heterocyclyl group is a 5–6 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–6 membered heterocyclyl”).
  • the 5–6 membered heterocyclyl has 1–3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5–6 membered heterocyclyl has 1–2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5–6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • Exemplary 3–membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, and thiorenyl.
  • Exemplary 4–membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl, and thietanyl.
  • Exemplary 5–membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl,
  • Exemplary 5– membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one.
  • Exemplary 5–membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplary 6–membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl.
  • Exemplary 6–membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl.
  • Exemplary 6– membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl.
  • Exemplary 7–membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl, and thiepanyl.
  • Exemplary 8–membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl, and thiocanyl.
  • Exemplary 5-membered heterocyclyl groups fused to a C 6 aryl ring include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like.
  • Exemplary 6-membered heterocyclyl groups fused to an aryl ring include, without limitation, tetrahydroquinolinyl,
  • Aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having 6–14 ring carbon atoms and zero heteroatoms in the aromatic ring system (“C 6–14 aryl”).
  • an aryl group has six ring carbon atoms (“C6 aryl”; e.g., phenyl).
  • an aryl group has ten ring carbon atoms (“C 10 aryl”; e.g., naphthyl such as 1–naphthyl and 2–naphthyl).
  • an aryl group has fourteen ring carbon atoms (“C14 aryl”; e.g., anthracyl).“Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system.
  • each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents.
  • the aryl group is unsubstituted C6–14 aryl.
  • the aryl group is substituted C6–14 aryl.
  • “Arylalkyl” is a subset of alkyl and aryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group.
  • the aralkyl is optionally substituted benzyl.
  • the aralkyl is benzyl.
  • the aralkyl is optionally substituted phenethyl.
  • the aralkyl is phenethyl.
  • Heteroaryl refers to a radical of a 5–10 membered monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 ⁇ electrons shared in a cyclic array) having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–10 membered heteroaryl”).
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • “Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system.
  • “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system.
  • Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom e.g., indolyl, quinolinyl, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2–indolyl) or the ring that does not contain a heteroatom (e.g., 5– indolyl).
  • a heteroaryl group is a 5–10 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–10 membered heteroaryl”).
  • a heteroaryl group is a 5–8 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–8 membered heteroaryl”).
  • a heteroaryl group is a 5–6 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–6 membered heteroaryl”).
  • the 5–6 membered heteroaryl has 1–3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5–6 membered heteroaryl has 1–2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5–6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a“substituted heteroaryl”) with one or more substituents.
  • the heteroaryl group is unsubstituted 5–14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5–14 membered heteroaryl.
  • Exemplary 5–membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl.
  • Exemplary 5–membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl.
  • Exemplary 5–membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
  • Exemplary 5–membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6–membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl.
  • Exemplary 6–membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • Exemplary 6–membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively.
  • Exemplary 7–membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl.
  • Exemplary 5,6–bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
  • Exemplary 6,6– bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Heteroaralkyl is a subset of alkyl and heteroaryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, which are divalent bridging groups are further referred to using the suffix– ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.
  • the term“optionally substituted” refers to a substituted or unsubstituted moiety.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are optionally substituted (e.g.,“substituted” or“unsubstituted” alkyl, “substituted” or“unsubstituted” alkenyl,“substituted” or“unsubstituted” alkynyl, “substituted” or“unsubstituted” carbocyclyl,“substituted” or“unsubstituted” heterocyclyl, “substituted” or“unsubstituted” aryl or“substituted” or“unsubstituted” heteroaryl group).
  • the term“substituted”, whether preceded by the term“optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound.
  • the present present disclosure contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • each instance of R aa is, independently, selected from C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two R aa groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R cc is, independently, selected from hydrogen, C 1–10 alkyl, C 1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two R cc groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R ee is, independently, selected from C1–6 alkyl, C1–6 perhaloalkyl, C2– 6 alkenyl, C 2–6 alkynyl, C 3–10 carbocyclyl, C 6–10 aryl, 3–10 membered heterocyclyl, and 3–10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups;
  • each instance of R ff is, independently, selected from hydrogen, C1–6 alkyl, C1–6 perhaloalkyl, C2–6 alkenyl, C2–6 alkynyl, C3–10 carbocyclyl, 3–10 membered heterocyclyl, C6– 10 aryl and 5–10 membered heteroaryl, or two R ff groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups; and
  • Halo or“halogen” refers to fluorine (fluoro,–F), chlorine (chloro,–Cl), bromine (bromo,–Br), or iodine (iodo,–I).
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms.
  • the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group).
  • Nitrogen protecting groups are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • nitrophenyl)propanamide 2–methyl–2–(o–nitrophenoxy)propanamide, 2–methyl–2–(o– phenylazophenoxy)propanamide, 4–chlorobutanamide, 3–methyl–3–nitrobutanamide, o– nitrocinnamide, N–acetylmethionine derivative, o–nitrobenzamide, and o–
  • Nitrogen protecting groups such as carbamate groups include, but are not limited to, methyl carbamate, ethyl carbamante, 9–fluorenylmethyl carbamate (Fmoc), 9–(2–sulfo)fluorenylmethyl carbamate, 9–(2,7–dibromo)fluoroenylmethyl carbamate, 2,7–di–t–butyl–[9–(10,10–dioxo–10,10,10,10–tetrahydrothioxanthyl)]methyl carbamate (DBD–Tmoc), 4–methoxyphenacyl carbamate (Phenoc), 2,2,2–trichloroethyl carbamate (Troc), 2–trimethylsilylethyl carbamate (Teoc), 2–phenylethyl carbamate (hZ), 1- (1-Adamantyl)
  • triphenylphosphonioisopropyl carbamate Ppoc
  • 1,1–dimethyl–2–cyanoethyl carbamate 1,1–dimethyl–2–cyanoethyl carbamate
  • m chloro–p–acyloxybenzyl carbamate
  • p (dihydroxyboryl)benzyl carbamate
  • benzisoxazolylmethyl carbamate 2–(trifluoromethyl)–6–chromonylmethyl carbamate (Tcroc), m–nitrophenyl carbamate, 3,5–dimethoxybenzyl carbamate, o–nitrobenzyl carbamate, 3,4–dimethoxy–6–nitrobenzyl carbamate, phenyl(o–nitrophenyl)methyl carbamate, t–amyl carbamate, S–benzyl thiocarbamate, p–cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p– decyloxybenzyl carbamate, 2,2–dimethoxyacylvinyl carbamate, o–(N,N–
  • methoxybenzenesulfonamide (Mte), 4–methoxybenzenesulfonamide (Mbs), 2,4,6– trimethylbenzenesulfonamide (Mts), 2,6–dimethoxy–4–methylbenzenesulfonamide (iMds), 2,2,5,7,8–pentamethylchroman–6–sulfonamide (Pmc), methanesulfonamide (Ms), ⁇ – trimethylsilylethanesulfonamide (SES), 9–anthracenesulfonamide, 4–(4 ⁇ ,8 ⁇ –
  • DMBS dimethoxynaphthylmethylbenzenesulfonamide
  • benzylsulfonamide benzylsulfonamide
  • nitrogen protecting groups include, but are not limited to, phenothiazinyl– (10)–acyl derivative, N ⁇ –p–toluenesulfonylaminoacyl derivative, N ⁇ –phenylaminothioacyl derivative, N–benzoylphenylalanyl derivative, N–acetylmethionine derivative, 4,5–diphenyl– 3–oxazolin–2–one, N–phthalimide, N–dithiasuccinimide (Dts), N–2,3–diphenylmaleimide, N–2,5–dimethylpyrrole, N–1,1,4,4–tetramethyldisilylazacyclopentane adduct (STABASE), 5–substituted 1,3–dimethyl–1,3,5–triazacyclohexan–2–one, 5–substituted 1,3–dibenzyl– 1,3,5–triazacyclohexan–2–one,
  • benzenesulfenamide o–nitrobenzenesulfenamide (Nps), 2,4–dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2–nitro–4–methoxybenzenesulfenamide,
  • triphenylmethylsulfenamide triphenylmethylsulfenamide
  • 3–nitropyridinesulfenamide Npys
  • the substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group).
  • Oxygen protecting groups are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t–butylthiomethyl,
  • methoxybenzyloxymethyl (PMBM), (4–methoxyphenoxy)methyl (p–AOM), guaiacolmethyl (GUM), t–butoxymethyl, 4–pentenyloxymethyl (POM), siloxymethyl, 2– methoxyethoxymethyl (MEM), 2,2,2–trichloroethoxymethyl, bis(2–chloroethoxy)methyl, 2– (trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3–
  • DPMS diphenylmethylsilyl
  • TMPS t–butylmethoxyphenylsilyl
  • TMSEC trimethylsilylethyl carbonate
  • Psec phenylsulfonyl ethyl carbonate
  • Peoc triphenylphosphonio ethyl carbonate
  • BOC t–butyl carbonate
  • p–nitrophenyl carbonate benzyl carbonate, p– methoxybenzyl carbonate, 3,4–dimethoxybenzyl carbonate, o–nitrobenzyl carbonate, p– nitrobenzyl carbonate, S–benzyl thiocarbonate, 4–ethoxy–1–napththyl carbonate, methyl dithiocarbonate, 2–iodobenzoate, 4–azidobutyrate, 4–nitro–4–methylpentanoate, o–
  • dimethylphosphinothioyl dimethylphosphinothioyl, alkyl 2,4–dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).
  • the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group).
  • protecting groups and in particular sulfur protecting groups, are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference in its entirety.
  • the term“leaving group” is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile.
  • suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, and haloformates.
  • the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate,–OTs), methanesulfonate (mesylate,– OMs), p-bromobenzenesulfonyloxy (brosylate,–OBs), or trifluoromethanesulfonate (triflate, –OTf).
  • the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy.
  • the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy.
  • the leaving group is a sulfonate-containing group.
  • glycan refers to a polysaccharide, oligosaccharide or monosaccharide. Glycans can be monomers or polymers of sugar residues and can be linear or branched. A glycan may include natural sugar residues (e.g., glucose, N- acetylglucosamine, N-acetyl neuraminic acid, galactose, mannose, fucose, hexose, arabinose, ribose, xylose, etc.) and/or modified sugars (e.g., 2′-fluororibose, 2′-deoxyribose,
  • natural sugar residues e.g., glucose, N- acetylglucosamine, N-acetyl neuraminic acid, galactose, mannose, fucose, hexose, arabinose, ribose, xylose, etc.
  • modified sugars e.g.
  • Glycans can be homo or heteropolymers of monosaccharide residues, and can be linear or branched. Glycans can be found attached to proteins as in glycoproteins and proteoglycans. They are generally found on the exterior surface of cells. O- and N-linked glycans are very common in eukaryotes but may also be found, although less commonly, in prokaryotes.
  • the terms“fucose”,“core fucose” and“ core fucose residue” are used interchangeably and refer to a fucose in ⁇ 1,6-position linked to the N- acetylglucosamine.
  • the terms“N-glycan”,“N-linked glycan”,“N-linked glycosylation”, “Fc glycan” and“Fc glycosylation” are used interchangeably and refer to an N-linked oligosaccharide attached by an N-acetylglucosamine (GlcNAc) linked to the amide nitrogen of an asparagine residue in a Fc-containing polypeptide.
  • the term“Fc-containing polypeptide” refers to a polypeptide, such as an antibody, which comprises an Fc region.
  • the term“glycosylation pattern” and“glycosylation profile” are used interchangeably and refer to the characteristic“fingerprint” of the N-glycan species that have been released from a glycoprotein or antibody, either enzymatically or chemically, and then analyzed for their carbohydrate structure, for example, using LC-HPLC, or MALDI-TOF MS, and the like. See, for example, the review in Current Analytical Chemistry, Vol.1, No.1 (2005), pp.28-57; herein incorporated by reference in its entirety.
  • A“defined glycan probe location” as used herein is a predefined region of a solid support to which a density of glycan molecules, all having similar glycan structures, is attached.
  • the terms“glycan region,” or“selected region”, or simply“region” are used interchangeably herein for the term defined glycan probe location.
  • the defined glycan probe location may have any convenient shape, for example, circular, rectangular, elliptical, wedge- shaped, and the like.
  • a defined glycan probe location and, therefore, the area upon which each distinct glycan type or a distinct group of structurally related glycans is attached is smaller than about 1 cm 2 , or less than 1 mm 2 , or less than 0.5 mm 2 . In some embodiments the glycan probe locations have an area less than about 10,000 ⁇ m 2 or less than 100 ⁇ m 2 .
  • the glycan molecules attached within each defined glycan probe location are substantially identical. Additionally, multiple copies of each glycan type are present within each defined glycan probe location. The number of copies of each glycan types within each defined glycan probe location can be in the thousands to the millions.
  • the arrays of the present disclosure have defined glycan probe locations, each with“one type of glycan molecule.”
  • The“one type of glycan molecule” employed can be a group of substantially structurally identical glycan molecules or a group of structurally similar glycan molecules. There is no need for every glycan molecule within a defined glycan probe location to have an identical structure.
  • the glycans within a single defined glycan probe location are structural isomers, have variable numbers of sugar units or are branched in somewhat different ways.
  • the glycans within a defined glycan probe location have substantially the same type of sugar units and/or approximately the same proportion of each type of sugar unit.
  • the types of substituents on the sugar units of the glycans within a defined glycan probe location are also substantially the same.
  • Detection of binding can be direct, for example, by detection of a label directly attached to the test molecule.
  • detection can be indirect, for example, by detecting a labeled secondary antibody or other labeled molecule that can bind to the test molecule.
  • the bound label can be observed using any available detection method.
  • an array CCD analyzer can be employed to detect chemiluminescence labeled molecules that are bound to array.
  • the term“antigen” is defined as any substance capable of eliciting an immune response.
  • immunogenicity refers to the ability of an immunogen, antigen, or vaccine to stimulate an immune response.
  • epitopope is defined as the parts of an antigen molecule which contact the antigen binding site of an antibody or a T cell receptor.
  • vaccine refers to a preparation that contains an antigen, consisting of whole disease-causing organisms (killed or weakened) or components of such organisms, such as proteins, peptides, or polysaccharides, that is used to confer immunity against the disease that the organisms cause.
  • Vaccine preparations can be natural, synthetic or derived by recombinant DNA technology.
  • the term“antigen specific” refers to a property of a cell population such that supply of a particular antigen, or a fragment of the antigen, results in specific cell proliferation.
  • An“isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with research, diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of, for example, a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using, for example, Coomassie blue or silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • support or“substrate” as used interchangeably herein refers to a material or group of materials, comprising one or a plurality of components, with which one or more molecules are directly or indirectly bound, attached, synthesized upon, linked, or otherwise associated.
  • a support may be constructed from materials that are biological, non-biological, inorganic, organic or a combination of these.
  • a support may be in any appropriate size or configuration based upon its use within a particular embodiment.
  • Target refers to a species of interest within an assay.
  • Targets may be naturally occurring or synthetic, or a combination.
  • Targets may be unaltered (e.g., utilized directly within the organism or a sample thereof), or altered in a manner appropriate for the assay (e.g., purified, amplified, filtered).
  • Targets may be bound through a suitable means to a binding member within certain assays.
  • targets include, but are not restricted to, antibodies or fragments thereof, cell membrane receptors, monoclonal antibodies and antisera reactive with specific antigenic determinants (such as on viruses, cells or other materials), drugs, oligonucleotides, nucleic acids, peptides, cofactors, sugars, lectins polysaccharides, cells, cellular membranes, and organelles.
  • Target may be any suitable size depending on the assay.
  • phrase“substantially similar,”“substantially the same”,“equivalent”, or “substantially equivalent”, as used herein, denotes a sufficiently high degree of similarity between two numeric values (for example, one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values, anti-viral effects, etc.).
  • the difference between said two values is, for example, less than about 50%, less than about 40%, less than about 30%, less than about 20%, and/or less than about 10% as a function of the value for the reference/comparator molecule.
  • the phrase“substantially reduced,” or“substantially different”, as used herein, denotes a sufficiently high degree of difference between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values).
  • the difference between said two values is, for example, greater than about 10%, greater than about 20%, greater than about 30%, greater than about 40%, and/or greater than about 50% as a function of the value for the reference/comparator molecule.
  • Binding affinity generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein,“binding affinity” refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd). Affinity can be measured by common methods known in the art, including those described herein.
  • “Polynucleotide,” or“nucleic acid,” as used interchangeably herein, refer to polymers of nucleotides of any length, and include DNA and RNA.
  • the nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer.
  • the sequence of nucleotides may be interrupted by non-nucleotide components.
  • a polynucleotide may be further modified after synthesis, such as by conjugation with a label.
  • modifications include, for example,“caps,” substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well
  • any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports.
  • the 5′ and 3′ terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms.
  • Other hydroxyls may also be derivatized to standard protecting groups.
  • Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2′-O-methyl-, 2′-O-allyl, 2′-fluoro- or 2′-azido-ribose, carbocyclic sugar analogs, ⁇ -anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and basic nucleoside analogs such as methyl riboside.
  • One or more phosphodiester linkages may be replaced by alternative linking groups.
  • linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(O)S (“thioate”), P(S)S (“dithioate”),“(O)NR2 (“amidate”), P(O)R, P(O)OR′, CO or CH2 (“formacetal”), in which each R or R′ is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
  • “Oligonucleotide,” as used herein, generally refers to short, generally single- stranded, generally synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length.
  • the terms“oligonucleotide” and“polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
  • “Antibodies” (Abs) and“immunoglobulins” (IGs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which generally lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
  • antibody and“immunoglobulin” are used interchangeably in the broadest sense and include monoclonal antibodies (e.g., full length or intact monoclonal antibodies), polyclonal antibodies, monovalent, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies so long as they exhibit the desired biological activity) and may also include certain antibody fragments (as described in greater detail herein).
  • An antibody can be chimeric, human, humanized and/or affinity matured.
  • The“variable region” or“variable domain” of an antibody refers to the amino- terminal domains of heavy or light chain of the antibody. These domains are generally the most variable parts of an antibody and contain the antigen-binding sites.
  • variable refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR).
  • CDRs complementarity-determining regions
  • FR framework
  • the variable domains of native heavy and light chains each comprise four FR regions, largely adopting a beta-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the beta-sheet structure.
  • the CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, Md. (1991)).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called“Fab” fragments, each with a single antigen-binding site, and a residual“Fc” fragment, whose name reflects its ability to crystallize readily.
  • Pepsin treatment yields an F(ab′)2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
  • “Fv” is the minimum antibody fragment which contains a complete antigen- recognition and -binding site.
  • this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association.
  • one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a“dimeric” structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer.
  • the six CDRs confer antigen-binding specificity to the antibody.
  • a single variable domain or half of an Fv comprising only three CDRs specific for an antigen
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain.
  • Fab′ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region.
  • Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab′)2 antibody fragments originally were produced as pairs of Fab′ fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • The“light chains” of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa ( ⁇ ) and lambda ( ⁇ ), based on the amino acid sequences of their constant domains.
  • antibodies can be assigned to different classes.
  • immunoglobulins There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2.
  • the heavy chain constant domains that correspond to the different classes of immunoglobulins are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • An antibody may be part of a larger fusion molecule, formed by covalent or non-covalent association of the antibody with one or more other proteins or peptides.
  • full length antibody “intact antibody” and“whole antibody” are used herein interchangeably, to refer to an antibody in its substantially intact form, not antibody fragments as defined below.
  • an antibody fragment comprises only a portion of an intact antibody, wherein the portion retains at least one, and as many as most or all, of the functions normally associated with that portion when present in an intact antibody.
  • an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen.
  • an antibody fragment for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half- life modulation, ADCC function and complement binding.
  • an antibody fragment is a monovalent antibody that has an in vivo half-life substantially similar to an intact antibody.
  • such an antibody fragment may comprise an antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment.
  • the term“monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts.
  • the modifier“monoclonal” indicates the character of the antibody as not being a mixture of discrete antibodies.
  • Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences.
  • the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones.
  • the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this present disclosure.
  • each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
  • the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins.
  • the modifier“monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present disclosure may be made by a variety of techniques, including, for example, the hybridoma method (e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Pat.
  • the hybridoma method e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell hybridomas 563-681 (Elsevier
  • phage display technologies See, e.g., Clackson et al., Nature, 352: 624-628 (1991); Marks et al., J. Mol. Biol.222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2): 299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al., J. Immunol.
  • Methods 284(1-2): 119-132 (2004), and technologies for producing human or human-like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences see, e.g., WO98/24893; WO96/34096; WO96/33735; WO91/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993); Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Pat. Nos.
  • the monoclonal antibodies herein specifically include“chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No.4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).
  • “Humanized” forms of non-human (e.g., murine) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin.
  • a humanized antibody is a human immunoglobulin (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity.
  • donor antibody such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity.
  • framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
  • the humanized antibody optionally will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • normal levels can be, for example, a reference value or range based on measurements of the levels of TACA bound antibodies in samples from normal patients or a population of normal patients.
  • Normal levels can also be, for example, a reference value or range based on measurements of the TACAs in samples from normal patients or a population of normal patients.
  • a“subject” is a mammal. Such mammals include domesticated animals, farm animals, animals used in experiments, zoo animals and the like. In some embodiments, the subject is a human.
  • A“disorder” is any condition that would benefit from treatment with an antibody of the present disclosure. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question.
  • disorders to be treated herein include HIV.
  • a transport enhancer encompasses a plurality of transport enhancers as well as a single transport enhancer.
  • Reference to "a chelating agent” includes reference to two or more chelating agents as well as a single chelating agent, and so forth. In this specification and in the claims that follow, reference will be made to a number of terms, which shall be defined to have the following meanings:
  • treating and “treatment” as used herein refer to the administration of an agent or formulation to a clinically symptomatic individual afflicted with an adverse condition, disorder, or disease, so as to effect a reduction in severity and/or frequency of symptoms, eliminate the symptoms and/or their underlying cause, and/or facilitate improvement or remediation of damage.
  • preventing and “prevention” refer to the administration of an agent or composition to a clinically asymptomatic individual who is susceptible to a particular adverse condition, disorder, or disease, and thus relates to the prevention of the occurrence of symptoms and/or their underlying cause. Unless otherwise indicated herein, either explicitly or by implication, if the term “treatment” (or “treating”) is used without reference to possible prevention, it is intended that prevention be encompassed as well.
  • pharmaceutically acceptable is meant a material that is not biologically or otherwise undesirable, e.g., the material may be incorporated into a formulation of the present disclosure without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the dosage form formulation.
  • pharmaceutically acceptable when used to refer to a pharmaceutical excipient, it is implied that the excipient has met the required standards of toxicological and manufacturing testing and/or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration.
  • pharmaceutically active or simply “active” as in a “pharmacologically active” derivative or analog refers to derivative or analog having the same type of pharmacological activity as the parent agent.
  • the term“antigen” is defined as any substance capable of eliciting an immune response.
  • the term“immunogen” refers to an antigen or a substance capable of inducing production of an antigen, such as a DNA vaccine.
  • the present disclosure provides libraries and arrays of glycans that can be used for identifying which types of proteins, receptors, antibodies, lipids, nucleic acids, carbohydrates and other molecules and substances can bind to a given glycan structure.
  • the arrays and methods of the present disclosure also provide highly accurate results.
  • the libraries and arrays of the present disclosure provide large numbers and varieties of glycans.
  • the libraries and arrays of the present disclosure have at least one, at least two, at least three, at least ten, or at least 100 glycans.
  • the libraries and arrays of the present disclosure have about 1 to about 100,000, or about 1 to about 10,000, or about 1 to about 1,000, or about 1 to about 100, or about 2 to about 100, or about 2 to about 10, or about 1 to about 10 different glycans per array.
  • Such large numbers of glycans permit the simultaneous assay of a multitude of glycan types.
  • the present arrays have been used for successfully screening a variety of glycan binding proteins.
  • the composition of glycans on the arrays of the present disclosure can be varied as appropriate.
  • Many different glyconjugates can be incorporated into the arrays of the present disclosure including, for example, naturally occurring or synthetic glycans, glycoproteins, glycopeptides, glycolipids, bacterial and plant cell wall glycans and the like.
  • Exemplary arrays configured suitably in accordance with various embodiments of the present disclosure include, for example, U.S. Patent No. US8383554 B2,“Quantitative Microarray of Intact Glycolipid CD1d Interaction and Correlation with Cell-Based Cytokine Production,” U.S. Patent No. US 8906832 B2 “QUANTITATIVE ANALYSIS OF CARBOHYDRATE-PROTEIN INTERACTIONS USING GLYCAN MICROARRAYS: DETERMINATION OF SURFACE AND SOLUTION DISSOCIATION CONSTANTS,” U.S. Patent No. US8680020 B2“Glycan arrays on PTFE-like aluminum coated glass slides and related methods,” U.S. Patent No.
  • the substrate may be, in some embodiments, a surface, solid surface, non- transparent solid, a solid transparent to selected wavelengths of visible or non-visible light, a particle, an array, a microbubble, or a bead.
  • the bead can be on a surface, embedded in a surface, or connected to a surface.
  • the substrate may be coated.
  • the substrate of the present disclosure can be a surface.
  • the surface can be flat, featured, round, curved, rough, porous, solid, gelatinous, polymeric, oligomeric, or a bead.
  • the substrate can be composed of glass, polymer, or plastic.
  • the bead can be round, cylindrical, egg-shaped, oval, approximately round, disc-shaped, square-shaped, hexagonal- shaped, or any polyhedral-shaped entity.
  • the substrate can be chemically modified so as to present a reactive group at the surface capable of binding to another molecule.
  • the reactive group can be a carboxylic acid.
  • the bead can be a silica bead.
  • the bead can be a silica-functionalized coated silica bead.
  • the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized silane molecule.
  • the functionalized silane molecule can be a functionalized trichlorosilane, functionalized dichlorisilane, or functionalized monochlorosilane molecule.
  • the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized tri-alkoxy functionalized silane.
  • the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized di-alkoxy functionalized silane. In some embodiments, the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized mono-alkoxy functionalized silane.
  • the functionalization can be an amino, aldehyde, halide, epoxy, NHS (N-hydroxy succinimide), maleimide, alkynyl, ethynyl, carbonyl (including carboxyl) or hydroxyl functional group.
  • the functionalization can be contacted with the silane via an C 1 -C 6 alkyl group, alkoxy group, or aryl group.
  • each glycan can be adhered to a specific bead type, so as to form a glycan-specific association with that bead type.
  • the bead can further comprise a distinct marker which distinguishes that particular bead type from other bead types.
  • a plurality of different glycans, each adhered to a distinct bead type can be mixed in a multiplex reaction.
  • the bead types and multiplex reaction detection methods can be those described in U.S. Patent No. 6,696,304 and PCT Patent App. No. PCT/US2004/038416, both of which are herein incorporated by reference.
  • the substrate can be coated with a material which can present a reactive group at the surface capable of binding to another molecule.
  • the material coating the substrate is a nitrocellulose membrane or a polymer.
  • Such coatings present a 3D surface with high surface area, enabling a lower limit of detection compared to flat surfaces.
  • an avidin, streptavidin, or neutravidin protein can be presented to the coated surface, such as a nitrocellulose membrane coating, for the attachment of biotinylated molecules.
  • a chemical linker can be presented to the surface, either directly to the surface or to a coating previously presented to the surface.
  • the present disclosure provides linkers that may be used in a variety of applications.
  • the linkers of the present disclosure may be used to attach molecules to substrates, such as surfaces, solid surfaces, particles, arrays or beads.
  • the present disclosure relates to a bead for use in disease diagnosis and drug discovery, the bead comprising: (a) a unique identifier on or within each bead; and (b) a glycan attached to the surface of the bead through a linker moiety.
  • the glycan can be any of the diverse glycans described herein.
  • the bead can be coated with a homogeneous population of glycan type.
  • the present disclosure relates to methods of making glycan- linker-beads, comprising (a) providing a bead comprising a unique identifier on or within each bead; (b) contacting a glycan-linker with the bead; and (c) forming a conjugate between the glycan-linker and the bead.
  • the unique indentifier on or within each bead can be a holographic image impregnated within the silica or glass bead, a specific amino acid sequence or oligonucleotide sequence attached to each bead, or a specific fluorophore attached to each bead.
  • the specific amino acid sequence or oligonucleotide sequence attached to each bead can be further linked to a linker moiety which is further conjugated to the specific glycan attached to each bead.
  • the present disclosure relates to glycan-linker beads made by a process comprising: (a) providing a bead comprising a unique identifier on or within each bead; (b) contacting a glycan-linker with the bead; and (c) forming a conjugate between the glycan-linker and the bead.
  • each glycan can be adhered to a specific bead type, so as to form a glycan-specific association with that bead type.
  • the bead can further comprise a distinct marker which distinguishes that particular bead type from other bead types.
  • the distinct marker can be an amino acid sequence, oligonucleotide sequence, fluorophore, or dye contacted to or within each bead type.
  • the fluorophore or dye can be those known within the art.
  • the amino acid sequence or oligonucleotide sequence can be detectected by an antibody or another oligonucleotide sequence complementary to the oligonucleotide sequence contacted to the bead.
  • the oligonucleotide sequence complimentary to the oligonucleotide sequence contacted to the bead surface can be labeled with one or a plurality of fluorophores.
  • the fluorophores can be any of those known in the art (e.g., FAM, Cy3, Cy5, Cy 7, Cy3.5, Cy5.5, BHQ quenchers, TAMRA, ROX, Texas Red, Alexa fluors, those described in the Molecular Probes/Invitrogen/ThermoFisher catalog as of the filing date of the present application, etc.).
  • a plurality of different glycans, each adhered to a distinct bead type can be mixed in a multiplex reaction.
  • arrays comprising unique libraries of different glycans adhered to defined regions on the solid support of an array surface can be adhered by any available procedure.
  • arrays are made by obtaining a library of glycan-linked glycopeptide molecules described herein, obtaining a substrate that has a surface modified to react with the specific linking moieties present on the glycan-linked glycopeptide molecules of the library and attaching the glycan molecules to the solid support by forming a van der Waals interaction between the linking moieties of the glycan-linked glycopeptide molecules and the modified surface of the substrate.
  • the modification reagent can be attached to the substrate via carbon-carbon bonds using, as a non-limiting example, siloxane bonds (using, for example, glass or silicon oxide, or activated silicon dioxide wherein the activated silicon dioxide is the result of the reaction of a silane molecule (e.g., those available from the Geleste, Inc. catalog as of the filing date of the present application, herein incorporated by reference), as the solid substrate).
  • siloxane bonds with the surface of the substrate are formed in via reactions of derivatization reagents bearing mono-, di-, or tri-chlorosilyl, or mono-, di-, or tri-alkoxysilyl groups.
  • the non-leaving (chloro- or alkoxy-) groups on the silane can be hydrocarbons.
  • the non-leaving groups can be linear or branched alkyl chains so as to form van der Waals interactions with the peptide chains of the glycan-linked glycopeptide.
  • the modification reagent can be applied to the substrate via other deposition methods known to those skilled in the art for applying coatings. Such methods include chemical vapor deposition, solution-phase deposition, Langmuir-Blodgett film formation, chemical plasma treatment to expose a reactive surface molecule, spin-coating, spray-drying, or electrospinning.
  • the modification reagent can be a polymer.
  • the polymer can be selected from polystyrene, polypropylene, polyethylene, polyethylimine, polycaprolactine, modified polycaprolactone, polymethyl methacrylate, polyacrylamide, poly-N,N-alkyl acrylamide, polyalkyl methacrylate, polyalkyl acrylate, a polysaccharide, or copolymers thereof.
  • the polysaccharide can be cellulose, nitrocellulose, chitosan, amylose, cellulose acetate, xanthan gum, dextran, welan gum, guar gum, gellan gum, diutan gum or pullulan.
  • the polysaccharide can further be functionalized by the reaction of an oxidizing group.
  • the oxidizing group can be sodium periodate.
  • the glycan can be reacted to the polysaccharide in the presence of a reducing agent.
  • the reducing agent can be a functionalized borohydride moiety.
  • the functionalized borohydride moiety can be a hydro-borohydride (e.g., sodium or potassium borohyride)), cyanoborohydride, or alkylborohydide moiety).
  • each type of glycan can be contacted or printed onto a solid support at a defined glycan probe location.
  • a microarray gene printer can be used for applying the various glycan-linked glycopeptide to defined glycan probe locations. For example, about 0.1 microliterto about 10 nanoliter (nL), or about 0.5 nL of glycan solution can be applied per defined glycan probe location or bead. Various concentrations of the glycan-linked glycopeptide solutions can be contacted or printed onto the solid support.
  • a glycan-linked glycopeptide solution of about 0.1 to about 1000 micromolar ( ⁇ M) glycan-linked glycopeptide or about 1.0 to about 500 ⁇ M glycan-linked glycopeptide or about 10 to about 100 ⁇ M glycan-linked glycopeptide can be employed.
  • ⁇ M micromolar
  • Such replicates provide internal controls that confirm whether or not a binding reaction between a glycan-linked glycopeptide and a test molecule is a real binding interaction.
  • Arrays of detector molecules are useful for detecting the presence of multiple analytes in a sample in parallel.
  • the elements of an array of detector molecules comprises a substrate, the presentation of a coating of a bio-active molecule on the substrate, the presentation of one or a plurality of analytes to the coated substrate, the formation of a complex between the analyte and the bio-active molecule on the substrate, and a mechanism of detection.
  • bio-active molecule means its ordinary meaning in the art and any molecule which exists or mimics a molecule known in biology or chemistry and which is capable of binding to another molecule via electrostatic, van der Waals interactions, hydrophobic interactions, covalent bonds, and/or hydrogen bonds.
  • the substrate of the current present disclosure can be a surface.
  • the surface can be flat, featured, round, curved, rough, porous, solid, gelatinous, polymeric, oligomeric, or a bead.
  • the substrate can be composed of glass, polymer, or plastic.
  • the bead can be round, cylindrical, egg-shaped, oval, approximately round, disc-shaped, square-shaped, hexagonal- shaped, or any polyhedral-shaped entity.
  • the substrate can be chemically modified so as to present a reactive group at the surface capable of binding to another molecule.
  • the reactive group can be a carboxylic acid.
  • the substrate can be coated with a material which can present a reactive group at the surface capable of binding to another molecule.
  • the material coating the substrate is a nitrocellulose membrane or a polymer.
  • Such coatings present a 3D surface with high surface area, enabling a lower limit of detection compared to flat surfaces.
  • a chemical linker can be presented to the surface, either directly to the surface or to a coating previously presented to the surface.
  • the substrate can be a functionalized bead as commercialized by Illumina, Inc. with the BeadXpress, or Luminex systems, as of the filing date of the present disclosure.
  • the exemplary method embodiment as disclosed herein is designed on the basis that diversity can be created by assembly of the so called “D1 and D2/D3 arm modules", followed by the ⁇ -specific mannosylation at the 3-O and/or 6-O position of the mannose residue of the common core trisaccharide.
  • oligomannose-type mono- to pentasaccharides, 1- 5
  • complex-type di- to heptasaccharides, 6-13
  • core trisaccharide 14-15 building blocks
  • the GlcNAc moiety of acceptor 16 was transformed into LacNAc by using ⁇ -1,4-galactosyltransferase and uridine 5’–diphosphogalactose (UDP-Gal) to form 21, which was further extended by ⁇ -2,6/2,3 sialyltransferase in the presence of cytidine-5’- monophospho-N-avetylneuraminic acid (CMP-Neu5Ac) to provide targets 23 and 24 respectively.
  • CMP-Neu5Ac monophospho-N-avetylneuraminic acid
  • Acceptor 21 was modified with the ⁇ -1,2-fucosyltransferase from HEK293 cells in the presence of guanosine 5’- diphospho- ⁇ -L-fucose (GDP-fucose) to provide 26 (Fig. 3a). It was observed that the ⁇ -1,2 fucosylated module 26 was accepted by the ⁇ -2, 6 sialyltransferase to give 27, but the ⁇ -2,3 sialyltransferase failed to accept this substrate (Fig.3a and Supplementary Scheme S23). Next, the symmetric modules 28-33 were prepared from acceptors 17-18 (Fig.3b).
  • acceptors 19-20 were designed in such a way that the GlcNAc at the mannose 2-O position was differentiated from the GlcNAc at the 4 or 6-O position by masking the 4-hydroxy group through acetylation to prevent enzymatic
  • a Gal residue was added by ⁇ - 1,4-GalT to the GlcNAc residue at the ⁇ -1,4 / 1,6 mannose branch, whereas the GlcNAc residue at the ⁇ -1,2 branch remained intact.
  • ⁇ -1,3- FucT and ⁇ -2, 6-SiaT were used for the preparation of the asymmetric modules 36-43, and 45- 47 (Fig.3c and Supplementary Scheme S25) which were purified and fully characterized (Supplementary III).
  • modules 21 and 22 were selected for the proof-of-concept experiment (Fig.4).
  • Peracetylation of modules 21 and 22, followed by transformation into the glycosyl fluoride provided donors 50 and 51 respectively.
  • the oligosaccharides with a preinstalled alkyl amine linker at the reducing end can be used directly for reaction with NHS (N-hydroxy succinimide, although epoxy functionalized slides would also work) slides through amide bond formation, or further modified or other array formats, or conjugated to proteins for structural and functional studies.
  • glycans I-XI (Fig. 5a) were linked to a phosphonic acid tail for spontaneous covalent immobilization on the ACG slide (Supplementary Scheme S21). After incubation with a secondary antibody, the inventorsdetermined the dissociation constant (K D.surf. )59 of the glycans interacting with the antibody of interest.
  • K D.surf. the dissociation constant
  • the signal intensity was enhanced, as shown by the use of PG16 at 1 ⁇ g/mL on the ACG slide in comparison to 25 ⁇ g/mL used on the NHS-coated glass slide (Fig. 5b and Supplementary Fig. S12).
  • PG9 showed an apparent specificity for the hybrid-type glycan (X) (Fig. 5b) and detectable binding to Man 5 GlcNAc 2 (IV) and the ⁇ 2,6-sialylated bi-antennary complex-type oligosaccharide (XI).
  • the inventors were unable to detect PG16 binding to Man 5 GlcNAc 2 .
  • the inventors have successfully developed a modular synthetic strategy for the rapid production of a diverse array of high-mannose-, hybrid- and complex-type N-linked oligosaccharides in highly pure and sufficient amounts, making possible the study of various N-glycans and the development of new glycan array platforms to determine the glycan specificities of newly discovered HIV-1 bNAbs.
  • the ACG array together with the binding measurements obtained in a high-throughput manner provide an effective means for detecting the extremely weak binding of HIV-1 bNAbs to glycans and enable the discovery and understanding of essential epitopes and hetero-ligands recognized by antibodies. These findings may aid speedy design of effective carbohydrate-based vaccines against HIV-1.
  • any of the terms“comprising”,“consisting essentially of”, and“consisting of” may be replaced with either of the other two terms in the specification.
  • the terms“comprising”,“including”, containing”, etc. are to be read expansively and without limitation.
  • the methods and processes illustratively described herein suitably may be practiced in differing orders of steps, and that they are not necessarily restricted to the orders of steps indicated herein or in the claims. It is also that as used herein and in the appended claims, the singular forms“a,”“an,” and“the” include plural reference unless the context clearly dictates otherwise.
  • the instant disclosure and examples herein documents the discovery of surprising efficacy and efficiency in synthesizing and generating N-glycans in arrays to achieve surprising efficacy in disease state (e.g. HIV-1) determination, prediction, and/or diagnosis.
  • disease state e.g. HIV-1
  • NMR Nomenclature The individual sugar residues of highmannose, hybrid and complex type oligosaccharides have been labeled as shown below.
  • the enzymes used in this work including Bacteroides fragilis L- fucokinase/GDP-fucose pyrophosphorylase (FKP), pyruvate kinase (PK), pyrophosphatase (PPA), cytidine monophosphate kinase (CMK), CMP-sialic acid synthetases (CSS) and ⁇ 1– 3-fucosyltransferase from Helicobacter pylori (Hp1–3FT ⁇ 26695) are examples of suitable recombinant enzymes that are expressed and purified in our laboratory. Enzymatic reactions with cofactor regeneration were carried out according to the procedure reported previously from our group 4 .
  • Method 1 for glycans with -Nphthallamide protection at all glucosamine residues: A mixture of protected glycans (50 mmol) and 10 mL of ethylene diamine: nBuOH (1:4) was stirred at 90 o C for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac 2 O/pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by flash column chromatography (acetone: toluene, 2/8, v/v). Product was de-acetylated using sodium methoxide in MeOH (10 mL) for overnight.
  • the reaction mixture was neutralized by using IR-120, filtered and concentrated in vacuo.
  • the residue was purified by flash column chromatography (acetone: toluene, 3/7, v/v). Product was dissolved in 10 mL MeOH: H 2 O: HCOOH (6:3:1), Pd(OH) 2 (50% by weight) was added and the reaction mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo.
  • the residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent, and the product was lyophilized to get desired oligosaccharides as a white color powder.
  • Method 2 for glycans with -NHTroc protection at all glucosamine residues: A mixture of protected glycans (50 mmol) and lithium hydroxide (250 mmol) in 10 mL of 1, 4 dioxane: H2O (4:1) was stirred at 90 o C for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac 2 O: pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by C18 gel column chromatography (MeOH: H 2 O as an eluent). The product was de-acetylated using sodium methoxide in MeOH (10 mL) for overnight.
  • the reaction mixture was neutralized by using IR-120, filtered and concentrated in vacuo.
  • the residue was purified by C18 gel column chromatography (MeOH: H2O as an eluent).
  • the product was dissolved in 10 mL MeOH: H2O: HCOOH (6:3:1), Pd(OH) 2 (50% by weight) was added and the mixture was hydrogenated for overnight.
  • the reaction mixture was filtered through Celite and concentrated in vacuo.
  • the residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent. The product was lyophilized to get desired oligosaccharides as a white color powder.
  • Enzymatic sialylation with cofactor regeneration Glycans (5 ⁇ mol), Neu5Ac (10 ⁇ mol), ATP (0.05 ⁇ mol), CTP (1 ⁇ mol), phosphoenolpyruvate (10 ⁇ mol, monopotassium salt), cytidine monophosphate kinase (CMK, 80 units), CMP-sialic acid synthetases (CSS, 120 units), pyruvate kinase (PK, 40 units), pyrophosphatase (PPA, 40 units) and ⁇ 2,6/2,3 sialyltransferase (150 units) were dissolved in 50 ⁇ mol Tris buffer (25 mM, pH 7.5).
  • reaction was incubated at 37 o C with gentle agitation. Complete consumption of starting material was confirmed by mass spectrometric analysis.
  • the reaction mixture was centrifuged and the supernatant subjected to gel filtration over P2-Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the respective products as amorphous white solids.
  • the mannosyl trichloroacetimidate building block 1 was obtained by reported procedure 5 .
  • the preparation of D1 arm trisaccharide 2 of Man 9 GlcNAc 2 began by glycosylation of mannosyl chloride S1a 6 and thioglycoside acceptor S1b 7 under the treatment of 2,6-di-tert- butylpyridine (DTBP) and silver triflate (AgOTf) to obtain disaccharide S1c (Scheme S1).
  • DTBP 2,6-di-tert- butylpyridine
  • AgOTf silver triflate
  • Zemplén deacetylation of S1c at 2-O position followed by glycosylation with S1a by employing DTBP and AgOTf gave desired trisaccharide S1e in 93% yield.
  • the leaving group modification of S1e from thioglycoside to glycosyl fluoride 2 was performed under the action of N-bromosuccinimide (NBS) and diethylaminosulfur trifluoride (DAST).
  • NBS N-bromosuccinimide
  • DAST diethylaminosulfur trifluoride
  • the fluoride transformation provided us better results in terms of ⁇ -selectivity and excellent yield during glycosylation with chitobiose trisaccharide.
  • AgOTf the condensation of donor S1a 6 and acceptor S1f 7 was performed to afford trimannose 3, which was subsequently deacetylated and further di-glycosylated with S1a to afford D2/D3 arm pentasaccharide 5 in 71% yield.
  • reaction mixture was neutralized with IR-120, filtered and concentrated in vacuo and the residue was purified by silica gel column chromatography (0% ⁇ 30% EA in hexane) to afford S1d (0.859 g, 89%) as a colorless oil.
  • reaction mixture was neutralized with IR-120, filtered and concentrated in vacuo and the residue was purified by silica gel column chromatography (0% ⁇ 25% EA in hexane) to afford S1g (1.10 g, 90%) as a colorless oil.
  • NIS (1.35 g, 6.01 mmol) and TfOH (66.2 ⁇ L, 0.75 mmol) were added slowly at -40 oC and stirred for 2 h until TLC (ethyl acetate: toluene, 1/9) indicated formation of product with consumption of starting material.
  • the reaction mixture was quenched with Et3N, filtered through Celite, and the filtrate was washed with aq. NaHCO3 (2 x 50 mL), aq.Na2S2O3 (2 x 50 mL) and finally with brine (50 mL) solution.
  • the organic layer was dried over Na2SO4 and concentrated in vacuo.
  • reaction mixture was stirred at room temperature for 2 h until TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of the starting material.
  • the reaction mixture was then filtered through Celite and concentrated in vacuo.
  • the residue was purified by flash column chromatography to afford 1-OH compound (0.980 g) as white color foam.
  • the residue (0.850 g, 0.608 mmol) was dissolved in CH2Cl2 (10 mL) at -30 oC, then DAST (160 ⁇ L, 1.21 mmol) was added slowly. The resulting reaction mixture was stirred for 1 h.
  • Preparation of sialylated D1 arm was achieved through coupling of two main building units S4c and S4d.
  • Use of sialyl phosphate donor S4a for the ⁇ -2,6 glycosylation of Gal S4b resulted in complete ⁇ -selectivity10.
  • the N-Phth protection at glucosamine of S2c was modified NHTroc, while doing so, the 4-OAc group was removed to afford the desired S4d.
  • the coupling of S4c and S4d afforded the desired tetrasaccharide, which further underwent anomeric modification to get donor 9.
  • reaction mixture was stirred at room temperature for 5 h until TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of the starting material.
  • the reaction mixture was then filtered through Celite and concentrated in vacuo.
  • the residue was purified by flash column chromatography (0% ⁇ 15% EA in toluene) to afford 1-OH compound (2.0 g) as white color foam.
  • the residue (2 g, 1.07 mmol) was dissolved in CH2Cl2 (10 mL) at - 30 oC, then DAST (284 ⁇ L, 2.14 mmol) was added slowly. The resulting reaction mixture was stirred for 1 h.
  • Pentasaccharides S5a and S5b were obtained according to our previous report3, in which the functional group was further modified from N-pthallamide to N-Troc. Finally, the anomeric p-methoxy phenyl group was removed and resulting–OH was changed to fluoride in presence of DAST.
  • step i A mixture of compound S5a and S5b (0.500 g, 0.212 mmole) and 10 mL of ethylene diamine: n-BuOH (1:4) was stirred at 90 oC overnight.
  • step ii Cerium ammonium nitrate (0.616 g, 0.725 mmol) was added to a solution of compound S5c or S5d (0.350 g, 0.145 mmol) in 10 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at 0 °C for 2 h. The reaction was diluted with EtOAc (100 mL) and washed with H2O (30 x 2 mL) and brine (30 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo.
  • reaction mixture was cooled to -50 oC, NIS (0.067 g, 0.302 mmol) and TfOH (4 ⁇ L, 0.037 mmol) were added slowly and resulting reaction mixture was stirred for 2 h.
  • the reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite, extracted with saturated Na2S2O3 followed by NaHCO3, dried over sodium sulfate and concentrated in vacuo.
  • the residue was purified by flash column chromatography (0% ⁇ 10% EA in toluene) to afford S7i (0.317 g, 73%) as colorless foam.
  • reaction mixture was then filtered and the organic layer washed with H2O (2 x 30 mL).
  • the aqueous layer was further extracted with CH2Cl2 (2 x 50 mL).
  • the combined organic layers were washed with brine solution (40 mL), dried over Na2SO4, and concentrated in vacuo.
  • the residue was purified by flash column chromatography (0% ⁇ 15% EA in toluene) to afford 15 (0.652 g, 70%) as colorless foam.
  • S12b was further glycosylated at the 6-O position with trimannosyl thioglycoside 3 and, then, activated by the stable radical cation tris(4-bromophenyl) ammoniumyl hexachloroantimonate in a one electron transfer reaction to afford nonasaccharide S12c.
  • compound S12c in hand, a series of functional group transformations were carried out to afford the desired fully deprotected glycan G12.
  • the precursor oligosaccharide G12 is an appropriate starting material for sialylation by ⁇ -2,6 or 2,3 sialyltransferase derived from marine bacteria, known for their broader acceptor specificity and no intrinsic sialidase activity.
  • Sialyl transferase (SiaT)-mediated enzymatic terminal sialylation1-4 of G12 efficiently permitted access to ⁇ - 2,6 and ⁇ -2,3 sialylated glycans G13 and G14, respectively (Scheme S12).
  • Cp2HfCl2 Bis(cyclopentadienyl) hafnium dichloride
  • AgOTf Silver
  • Compound S14c A mixture of silver triflate (0.067 g, 0.27 mmol), bis
  • Compound S14b acts as common acceptor for both G18 and G24. Glycosylation of S14b at 6-O site provided the desired S15a with 10% acceptor recovery. At last, global deprotection yielded the desired glycan G24.
  • Compound S15a A mixture of silver triflate (0.058 g, 0.23 mmol), bis
  • Compound 16a A mixture of silver triflate (0.087 g, 0.34 mmol), bis
  • Compound 16c A mixture of silver triflate (0.068 g, 0.34 mmol), bis
  • Glycan G29 is mono sialylated tetraantennary complex type structure. The synthesis began with construction of D1 arm by glycosylation of donot 11 at 3-O position of 15 to afford compound S17a. The reaction was progress was checked by TLC as shown in Scheme S17. Removal benzyledene followed by 6-O glycosylation afforded desired tetra- decasaccharide S17c. Finally, global deprotection provided desired glycan G29.
  • Compound S17a A mixture of silver triflate (0.173 g, 0.675 mmol), bis
  • Compound S17c A mixture of silver triflate (0.046 g, 0.180 mmol), bis
  • Compound S18a A mixture of silver triflate (0.051 g, 0.200 mmol), bis
  • Intermidiate S16b derived from scheme S16 was used for ⁇ -selective glycosylation using donor 13 in presence of AgOTf/Cp2HfCl2 to get S19a in 74% yield. However, the newly formed product was overlaped with acceptor on TLC (Scheme S19). S19a was then further deprotected to furnish glycan G31.
  • Compound S19a A mixture of silver triflate (0.042 g, 0.165 mmol), bis
  • the pauci mannose type structure bearing core fucose G312 was assembled from the reducing end disaccharide S20k through fucosylation of diol acceptor S20j by donor S20i (Scheme S20).
  • the ⁇ -selectivity was enhanced by in situ anomarization protocol (CuBr2, tetrabutyl ammonium bromide), which was first developed by Lemieux and co-workers14, to get disaccharide S20k in 67% yield with its regio- and stereo-chemistry confirmed by NMR analysis.
  • reaction mixture was cooled to -60 oC, 2,6-di-ter-butyl pyridine (268 ⁇ L, 1.24 mmol) followed by Tf2O (79 ⁇ L, 0.483 mmol) was added and stirred for 40 minutes.
  • a solution of acceptor S20b (0.2 g, 0.378 mmol) in CH2Cl2 (5 mL) was added slowly and the resulting reaction mixture was stirred for 1 h until TLC (ethyl acetate: toluene, 1/9) indicated formation of a product with consumption of the starting material.
  • the reaction mixture was quenched with Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo.
  • the reaction mixture was filtered through Celite and concentrated in vacuo.
  • the residue was purified by Bio-Gel P-2 (BIO- RAD) column chromatography using water as eluent.
  • the product was the lypholysed to obtain the desired sugar with phosphonic acid tail as white color powder.

Abstract

The present disclosure relates to novel modular methods for generating a diversity of N-glycans of high mannose, hybrid and complex types. The present disclosure also relates to exemplary arrays of the synthesized N-glycans spotted onto aluminium oxide coated slides. These arrays can be used to detect and analyze binding interactions between the synthesized N-glycansand glycan binding molecules, such as HIV-1 neutralizing antibodies. The present disclosure also relates to methods for identifying agents that bind to various types of molecules on the arrays and to defining the structural elements of the molecules on the arrays that bind to those agents. The arrays and methods provided herein may be used for general epitope identification, drug discovery and as analytical tools. The present disclosure also provides useful glycans and epitope determinants that are useful in detecting, diagnosing, recurrence monitoring and preventing pathological diseases such as HIV.

Description

Methods for Modular Synthesis of N-glycans and Arrays Thereof
CHI-HUEY WONG, CHUNG-YI WU and SACHIN S SHIVATARE
Related Application
[001] This application claims the benefit of priority to US provisional application No.
62/305,441 filed on March 8th 2016. The contents of which is incorporated by reference herein in its entirety.
FIELD
[002] The present disclosure is related generally to chemical and chemo-enzymatic methods for synthesis of highly diverse N-glycans of high mannose, hybrid and complex types, arrays made from said glycans, and use of said arrays. Specifically, the present disclosure relates to methods of synthesis of N-glycan arrays on aluminum oxide coated substrate using a novel modular N-glycans synthetic approach, and the use of said N-glycan arrays for detection and analysis of binding reactions by glycan-binding molecules such as broadly neutralizing HIV antibodies.
BACKGROUND
[003] N-linked glycosylation of proteins is a fundamental and important post-translational modification found both in eukaryotes and in prokaryotes. This protein modification results in the covalent attachment of an oligosaccharide onto asparagine residues of polypeptide chains. Glycans are typically the most important interface between cells and their environment. As a vital constituent of all living systems, glycans are involved in most of the essential biological processes such as protein folding, cell signaling, fertilization, embryogenesis, and the proliferation of cells and their organization into specific tissues. Abnormal cell surface glycosylation and/or glycan-profiles are usually related to diseases such as cancer and atherosclerosis. Accordingly, altered glycosylation is an indication of an early and possibly critical point in development of human pathologies. Thus, insights into the carbohydrate related biological and pathological processes, and for developing diagnostics and therapeutics for human diseases.
[004] The biosynthesis of complex oligosaccharides generally results in tremendous complexity and diversity, mainly due to the variable and multiple connectivity of glycan building blocks (monosaccharides). These cell-identifying glycosylated molecules include glycoproteins and glycolipids and are specifically recognized by various glycan binding molecules such as lectins, antiglycan antibodies, chemical compounds and also other glycans and glycolipids, etc. However, the enormous complexity of these interactions, and the lack of well-defined glycan libraries and analytical methods have been shown to be major obstacles in the development of glycomics. Moreover, naturally occurring glycans are typically isolated in tiny amounts and exist only as admixtures of isomers. As such, the limited availability and limited purity of said naturally occurring glycans do not allow their use as a reliable source of well-characterized oligosaccharides. Thus, novel synthesis methods are useful for the preparation of diverse glycan libraries for biological and structural applications.
[005] The development of nucleotide and protein microarrays has revolutionized genomic, gene expression and proteomic research. Similarly, the development of glycan microarrays has allowed an unprecedented high-throughput exploration of the specificities of a diverse range of glycan-binding molecules. The systematic arrangement of glycans on arrays allow for efficient probing of low affinity protein-glycan interactions through multivalent presentation. Since their establishment, various types of “arrays” have been developed, including the one available from the Consortium of Functional Glycomics (CFG) which contains more than 600 oligosaccharides on an N-hydroxysuccinimide (NHS)-activated glass slide. However, the spacer group and immobilization chemistry used in different array formats clearly result in differences in the density, distribution and orientation of glycan presentation, which dramatically affects the binding affinity and even specificity in glycan-protein interactions. Therefore, cross-comparison among different array platforms and development of new glycan arrays to improve the sensitivity of detection, for example, of hetero-ligand bindings are particularly important. Moreover, pharmaceutical companies and research institutions would greatly benefit from glycan arrays for various screening and drug discovery applications, including arrays that facilitate analysis of the structural elements of glycans that contribute to binding to glycan binding molecules including antibodies, receptors and other biomolecules.
SUMMARY
[006] The present disclosure provides compositions and methods of preparation of diverse N- linked oligosaccharides (N-glycans) of high mannose, hybrid and complex types. The methods of the present disclosure include chemical synthesis, and/or enzymatic synthesis. In certain embodiments, one or more of said synthesized N-glycans are spotted onto a substrate in a given area (known as a“spot”), wherein one or more of said spots are pooled to generate an N-glycan array for use in, for example, binding profiling, rapid screening and
identification of optimal glycans recognized by glycan-binding molecules, such as antibodies and viruses.
[007] In one aspect, the present disclosure provides the method wherein the strategically protected building blocks termed as“D1 and D2/D3 arm modules” can be regio- and stereospecifically glycosylated at the 3-O and/or 6-O position of the orthogonally protected Manβ1–4GlcNAcβ1–4GlcNAcβ1 core. In certain embodiments, the resulting glycans can be deprotected and/or unmasked in order to yield a final oligosaccharide product, or in certain embodiments, it can be selectively extended enzymatically to yield the final complex oligosaccharide products. In certain embodiments, the final oligosaccharide products are equipped with amino alkyl linker at the reducing end to restore its structural integrity and to act as handle for immobilization on arrays, or in certain other embodiments, said products can alternatively be conjugated to carrier proteins. [008] In one aspect, a preferred orthogonally protected Manβ1–4GlcNAcβ1–4GlcNAcβ1 core trisaccharide contains at least two ortho onal rotectin rou s, and has the formula (I)
Figure imgf000005_0001
Wherein each of R1, R2, R3, R4, R5, R6, R7, and R8 is independently selected from the group consisting of an orthogonal or a permanent protecting group; wherein, each of the orthogonal protecting group at R6 is preferably selected from para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), levulinoyl (Lev), benzoyl (Bz), allyl ether (Allyl), and silyl ethers; and R7 and R8 are fused to form benzylidene ring which can be cleaved to form either 4-OH and/or 6-OH;
Each of R2, R3, R4, and R5 is independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac);
R1 is a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac); or a protected fucoside residue connected via α 1,6 linkage;
X is–OR9; wherein R9 is–H or optionally substituted C3-C10 alkyls chain terminated with groups consisting of–N3 or NR10; and R10 is–H or benzyl (Bn) or carbobenzoyl (Cbz);
Y and Z are–NHR11; and R11 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) or tert-butoxycarbonyl (Boc).
[009] As used herein, a“permanent protecting group” can be a chemical moiety that prevents functionalization of a functional group when exposed to conditions which would normally functionalize said functional group. The permanent protecting group can be selectively removed to expose the functional group in the resulting molecule. In some aspects, the exposed functional group can be further reacted with another moiety, or can be left unfunctionalized.
[0010] In a second aspect, the preferred D1 and D2/D3 arm modules has the general formula (II)
Figure imgf000006_0001
Wherein, each of R1, R2, R3, and R4 is–H or a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
Figure imgf000006_0002
Wherein, Each of R5, R6, R7, and R8 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz);
Each of R9 and R10 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or a protected fucoside residue connected via α 1,3 linkage to GlcNAc and/or α 1,2 linkage to Galactose;
R11 is–H or Me, Et;
R12 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or protected Neu5Ac residue connected via α 2,6 linkage;
R13 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
Figure imgf000007_0001
X is–OR14 or–SR15
Wherein, R14 is H, alkyl, alkenyl, alkynyl, aryl or substituted aryl; a protecting group such as a silyl or substituted silyl, preferably thexyldimethylsilyl (TDS), t-butyldimethylsilyl (TBS), t- butyldiphenyl silyl (TBDPS), triisopropylsilyl (TIPS), trimethylsilyl (TMS), or triethylsilyl (TES); methyl (Me), acetyl (Ac), benzyl (Bn), 2-naphthylmethyl (Nap) or 1- naphthylmethyl (1-Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), allyl ether (Allyl), or an anomeric leaving group such as fluoride–F, trichloroacetimidate - C(NH)-CCl3, phenyltrifluoroacetimidate -C(NPh)-CF3, trifluoroacetimidate -C(NH)-CF3; thioalkyl, thiophenyl;
R15 is H, alkyl, aryl, or substituted aryl, preferably methyl, ethyl, phenyl, tosyl, or tolyl.
Y is –NHR16; and R16 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) or tert-butoxycarbonyl (Boc).
[0011] In accordance with said second aspect, the D1 and D2/D3 arm modules of general formula (II) are prepared chemically or preferably chemo-enzymatically.
[0012] In another embodiment of said second aspect, the examplars of chemically s nthesized D1 and D2/D3 arm modules are selected from the rou consistin of
Figure imgf000008_0001
[0013] In another embodiment of said second aspect, the chemo-enzymatic synthesis of D1 and D2/D3 arm modules commenced with chemically prepared acceptors substrates of formula (III)
Figure imgf000009_0001
Wherein,
each of R1 and R2 is independently selected from–H or the protecting groups acetyl (Ac) or benzoyl (Bz);
X is–OR3 and R3 is H, benzyl (Bn), 2-naphthylmethyl (Nap) or 1-naphthylmethyl (1- Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), allyl ether (Allyl).
[0014] In another embodiment of said second aspect, the chemo-enzymatically prepared acceptor substrates of formula (III) are subjected to enzymatic extensions, wherein the enzymes are independently selected from the group consisting of β (1→4)
Galactosyltransferase, α (1→3) Fucosyltransferase, α (1→2) Fucosyltransferase, β (1→3) N- acetyl glucosamine transferase, α (2→3) sialyltransferase, and α (2→6) sialyltransferase.
[0015] In another embodiment, the chemo-enzymatically prepared modules of formula (II) can be transformed into their acetates or benzoates form.
[0016] In another embodiment, the fully acetylated or benzoylated modules of formula (II) can undergo reducing end modification to form an anomeric leaving group such as trichloroacetimidate -C(NH)-CCl3, phenyltrifluoroacetimidate -C(NPh)-CF3,
trifluoroacetimidate -C(NH)-CF3; thioalkyl, thiophenyl, and more preferable fluoride–F.
[0017] In a third aspect, chemically or chemo-enzymatically prepared D1 and D2/D3 arm modules of formula (II) are independently selected for chemical glycosylation at 3-O and/or 6-O positions of Manβ1–4GlcNAcβ1–4GlcNAcβ1 core trisaccharide of formula (I).
[0018] The present disclosure also provides an orthogonally protected Manβ1–4GlcNAcβ1 core containing at least two orthogonal protecting groups, and has the formula (IV)
Figure imgf000010_0001
Wherein each of R1, R2, R3, R4, R5, and R6 is independently selected from the group consisting of an orthogonal or a permanent protecting groups; wherein, each of the orthogonal protecting groups at R4 is preferably selected from para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), levulinoyl (Lev), benzoyl (Bz), allyl ether (Allyl), and silyl ethers; and R5 and R6 are fused to form benzylidene ring which can be cleaved to form either 4-OH and/or 6-OH;
Each of R1, R2, and R3 is independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac);
X is–OR7; wherein R7 is–H or benzyl (Bn) or allyl (All);
Y is–NHR8; and R8 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) or tert-butoxycarbonyl (Boc).
[0019] In some embodiments, conditions effective to cause cleavage of each of the different orthogonal protecting groups preferably do not cause cleavage of other protecting groups present on the oligosaccharide building blocks.
[0020] The N-glycan core structure is optionally equipped with a spacer or linker and includes - (CH2)5NH2 at the reducing end to facilitate efficient immobilization on arrays and conjugation to carrier proteins. The present disclosure also provides spacers such as -(CH2) nNH-CO-O-[(CH2)2-O-(CH2)2]2-3-O-PO(OH)2 to facilitate efficient immobilization on aluminum oxide arrays through phosphonate chemistry. [0021] In another aspect, the present disclosure provides a method for making an orthogonally protected Manβ1–4GlcNAcβ1-4GlcNAcβ1 core.
[0022] In another aspect, the present disclosure provides chemical and chemo-enzymatic methods for making D1 and D2/D3 arm modules.
[0023] In one aspect, the present disclosure provides the strategy to prepare thousands of structurally-distinct complex N-linked oligosaccharides (N-glycans), wherein the material can be used for (1) development of glycan arrays to determine binding specificities of carbohydrate binding molecules such as lectins, galactose binding proteins (galectins), anti- glycan antibodies, HIV broadly neutralizing antibodies, and preferably of influenza hemagglutinin, chemical compounds and also other glycans and glycolipids; (2) standards for glycan sequencing using mass spectrometry; (3) preparation of diverse glycoforms at Fc- region of therapeutic antibodies such as Rituxan, Herceptin, Humira for enhancement of their effector functions; and (4) oligosaccharides standards for glycobiology research laboratories.
[0024] In one aspect, the present disclosure comprises an array of carbohydrate moieties immobilized on a substrate, the array comprising: a plurality of glycans wherein one or more glycan moieties are deposited at a discrete location (e.g. a spot) on the substrate, wherein the diverse glycans comprises homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types wherein the array is useful for the detection of hetero-glycan binding behavior.
[0025] In one aspect, the present disclosure comprises a method for detecting hetero-glycan binding behavior comprising contacting the array with one or a plurality of hetero-glycans. In some apsects, the hetero-glycans can be part of broadly neutralizing HIV-1 antibodies.
[0026] In certain embodiments, the glycans comprising homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types are prepared by modular chemo-enzymatic methods. In certain embodiments, the use of an array for the detection of hetero-glycan binding behavior comprises the steps of detecting binding specificity of broadly neutralizing HIV-1 antibodies.
[0027] In certain embodiments, the glycans comprises one or more of the compounds G1- G33 as set forth in Figure S11 and/or any one or more of the compounds I-XI as set forth in Figure S17.
[0028] In certain embodiments, the glycans can include or exclude one or more of the compounds G1-G33 as set forth in Figure S11 and includes or excludes any one or more of the compounds I-XI as set forth in Figure S17.
[0029] In another aspect, a method for synthesizing the glycan moieties of any one of claims 1-6 wherein the method of synthesis is based on or derived from synthetic schemes in part or in whole as set forth in Figures 1-4, is provided.
[0030] In another aspect, a method for generating vaccine targets comprising screening and identification of optimal cell surface glycans recognized by neutralizing HIV-1 antibodies, wherein the method further comprises contacting the HIV antibodies with the array of any one of claims 1-6, is provided.
[0031] In one aspect, a glycan microarray on an aluminium oxide-coated glass (ACG) slide, or an indium tin-oxide-coated (ITO) glass slide, containing a diverse set of glycans, including homo- and mixed N-glycans of high-mannose-, hybrid-, and complex- type prepared by modular chemo-enzymatic methods is provided. In certain embodiments, the array is useful for the detection of hetero-glycan binding behaviors.
[0032] In one related aspect, the method of generating/fabricating said glycan microarray is provided. In certain embodiments, synthetic strategy based on diversity can be created by assembly of the so called "D1 and D2/D3 arm modules", followed by the α-specific mannosylation at the 3-O and/or 6-O position of the mannose residue of the common core trisaccharide. [0033] In certain other embodiments, the glycosyl fluoride strategy was combined with enzymatic sialylation to build a library of symmetric bi-, tri- and tetraantennary complex-type glycans 50. In certain embodiments, modular synthetic methods for preparation of high mannose, hybrid and asymmetrically sialylated multi-antennary glycans are provided (e.g. Fig.1b).
[0034] In one aspect, a method for rapid screening and identification of optimal glycans recognized by neutralizing antibodies is provided. In certain embodiments, the screening directly facilitates development of HIV-1 vaccines targeting cell surface glycans.
[0035] In one aspect, this disclosure relates to screening libraries of glycan binding partners to identify N-glycan binding partners that bind to an array comprising one or more N-glycans as disclosed herein. In some aspects, the molecules in said libraries may comprise, for example, antibodies, nanobodies, antibody fragments, aptamers, lectins, peptides, biomolecules, or combinatorial library molecules. In one embodiment, said screening comprises a detection step, wherein the detection step comprises the detection of N-glycan binding by a HIV antibody. In one embodiment, the detection of said HIV antibody comprises the use of a N-glycan array, comprising one or more N-glycans as disclosed herein.
[0036] In one aspect, this disclosure relates to a method of of detecting N-glycan binding wherein a complex is formed by contacting the array with one or a plurality of N-glycans, and contacting the complex with a label. In some aspects, the label can then be detected. In some aspects, the label can be a labeled antibody. In some aspects, the labeled antibody can further comprise a label comprising an enzyme, fluorophore, a chemiluminescent moiety, or a nanoparticle.
[0037] In one aspect, this disclosure relates to a method of detecting HIV antibodies, the method comprising: providing an array of N-linked glycans as described herein, contacting the array with HIV antibodies; forming a complex between the HIV antibodies and the glycans on the array; contacting the HIV antibody-glycan array complex with a label; and detecting the label. In some aspects, the label can be a labeled antibody further comprising an enzyme, fluorophore, chemiluminescent moiety, or a nanoparticle.
[0038] In some embodiments, the array comprises a substrate and a multitude of defined glycan probe locations on the solid support, each glycan probe location defining a region of the solid support that has multiple copies of one or more type of similar glycan molecules attached thereto. In some embodiments, each glycan probe location defines a region of the solid support that has multiple copies of more than one types of similar glycan molecules attached thereto.
[0039] The interaction between A and X can, in some embodiments, be a covalent bond, Van der Waals interaction, hydrogen bond, ionic bond, or hydrophobic interaction.
[0040] The details of one or more embodiments of the present disclosure are set forth in the description below. Other features or advantages of the present disclosure will be apparent from the following drawings and detailed description of several embodiments, and also from the appending claims.
DESCRIPTION OF THE DRAWINGS
[0041] Figure 1 shows an exemplary general strategy for the modular synthesis of N-glycans. Due to the large number of possible glycosidic linkages and the generation of a diversity of structures, especially from the GlcNAc residues to the non-reducing end, a modular approach is used to minimize the reaction steps and create enough diversity to reflect the nature of N-glycosylation. FIG. 1A) The synthesis of high mannose-, hybrid-, and complex-type N-glycans through the regio- and stereoselective glycosidation of orthogonally protected core trisaccharide at the 3-O and 6-O positions with a modular set of diverse glycosyl donors. FIG.1B) The representative N-glycans that can be generated by this strategy FIG.1C) Retrosynthetic disconnections of high-mannose-, hybrid- and complex-type glycans showing the required building blocks for assembly.
[0042] Figure 2 shows exemplary structures of D1 and D2/D3 arm building blocks. A modular set of building blocks that are prepared by total chemical synthesis and used for oligosaccharide assembly.
[0043] Figure 3 shows exemplary chemo-enzymatic synthesis of modules. A representative chemo- enzymatic approach to the synthesis of FIG.3A, linear; FIG.3B, symmetric and FIG.3C, asymmetrically branched modules essential for N-glycan assembly. Reagents and conditions: i), UDP-galactose, β-1, 4-GalT; ii), GDP-fucose, α-1, 3-FucT; iii), CMP-Neu5Ac, α-2, 6-SiaT; iv), CMP-Neu5Ac, α-2, 3-SiaT; v), GDP-fucose, α-1, 2-FucT; vi), NaOH.
[0044] Figure 4 is a representative proof-of-concept demonstration of chemo-enzymatic strategy to N-glycan synthesis. Reagents and conditions. i), acetic anhydride, pyridine; ii), (1) CAN, toluene: ACN: H2O: toluene; (2) DAST, CH2Cl2, -30oC; iii), AgOTf, Cp2HfCl2, toluene, 4Å MS, 0oC to rt; iv), p-TSA, acetonitrile, rt; v), (1) LiOH, 1,4-dioxane: H2O; 90oC, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5: 3: 2), H2. CAN: Cerium ammonium nitrate; DAST: Diethylaminosulfur trifluoride; AgOTf: Silver
trifluromethanesulfonate; Cp2HfCl2: Bis(cyclopentadienyl)hafnium dichloride, MS: molecular sieves.
[0045] Figure 5 shows exemplary glycan specificities of HIV-1 bNAbs on ACG array. FIG 5A.), Synthetic N-glycans are chemically modified with a phosphonic acid tail for covalent attachment to the aluminium oxide-coated glass (ACG) slide through phosphonate chemistry. FIG.5B), FIG.5C), Binding of PG9, PG16 and PGTs 141-144 to structures I-XI printed on an ACG slide FIG.5D), FIG.5E), Binding of PG9 and PG16 to each of the glycan mixtures was evaluated to determine the effect of adjacent glycans on binding affinity. Arrays were printed by mixing 100 µM of
Man5GlcNAc2 or the complex-type glycan with every structure from I-XI in a 1:1 ratio. The molar concentrations in µM for antibodies are given in the legend. The mean signal intensities and standard error calculated for five independent replicates on the array are shown.
[0046] Figures 6A and 6B shows exemplary glycan specificities of PG9 (panel A– FIG.6A) and PG16 (panel B– FIG.6B) to mixture of Man5 and XI at various ratios. Arrays were printed by 100 µM of linker, Man5GlcNAc2 (IV), complex type glycan (XI) and each of the mixtures of (IV + XI) or (XI + IV) in a 1:1/2/3/4/5 ratio. The molar concentrations in µM for antibodies are given in the legend. The mean signal intensities and standard error calculated for eight independent replicates on the array are shown.
[0047] Figure 7 shows an exemplary structure embodiments of the present disclosure.
[0048] Figure 8 shows an exemplary structure embodiments of the present disclosure.
[0049] Figure 9 shows an exemplary structure embodiments of the present disclosure.
[0050] Figure 10 shows an exemplary structure embodiments of the present disclosure.
[0051] Figures 11A, 11B, and 11C: FIG.11A shows an exemplary structure embodiments of the present disclosure. FIG.11B shows an exemplary structure embodiments of the present disclosure. FIG.11C shows an exemplary structure embodiments of the present disclosure.
[0052] Figure 12 shows an exemplary structure embodiments of the present disclosure.
[0053] Figure 13 shows an exemplary structure embodiments of the present disclosure.
[0054] Figure 14 Exemplary Modular synthesis of high mannose, hybrid- and complex-type N-glycans.
[0055] Figure 15A to 15C Exemplary sugar residues of representative highmannose, hybrid and complex type oligosaccharides. (FIG.15A = High Mannose type; FIG.15B = hybrid type, FIG. 15C = complex type).
[0056] Figure 16 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0057] Figure 17 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0058] Figure 18 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0059] Figure 19 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0060] Figure 20 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0061] Figure 21 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0062] Figure 22 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0063] Figure 23 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0064] Figure 24 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0065] Figure 25 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0066] Figure 26 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0067] Figure 27 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0068] Figure 28 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0069] Figure 29 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0070] Figure 30 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0071] Figure 31 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0072] Figure 32A, 32B, and 32C: FIG.32A shows exemplary structure embodiments in a representative synthetic scheme embodiments of the present disclosure. FIG.32B shows exemplary structure embodiments in a representative synthetic scheme embodiments of the present disclosure. FIG.32C shows exemplary structure embodiments in a representative synthetic scheme
embodiments of the present disclosure.
[0073] Figure 33 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0074] Figure 34 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0075] Figure 35 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0076] Figure 36 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0077] Figure 37A, 37B and 37C: FIG.37A shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. FIG.37B shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. FIG.37C shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0078] Figure 38 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0079] Figure 39 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0080] Figure 40 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0081] Figure 41 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0082] Figure 42A and 42B: FIG.42A shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure. FIG.42B shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
[0083] Figure 43 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0084] Figure 44 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0085] Figure 45 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0086] Figure 46 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0087] Figure 47A, 47B and 47C: FIG.47A shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure. FIG.47B shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure. FIG.47C shows exemplary structure embodiments in a representative synthetic scheme embodiment of the present disclosure.
[0088] Figure 48 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0089] Figure 49 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0090] Figure 50 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0091] Figure 51 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0092] Figure 52 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0093] Figure 53 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0094] Figure 54 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. [0095] Figure 55 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0096] Figure 56 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0097] Figure 57 shows exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[0098] Figure 58 Exemplary Structures of high mannose type glycans and their fragments.
[0099] Figure 59A and 59B: FIG.59A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.59B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00100] Figure 60A and 60B: FIG.60A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.60B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00101] Figure 61 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00102] Figure 62 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00103] Figure 63 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00104] Figure 64 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00105] Figure 65 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00106] Figure 66 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00107] Figure 67 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00108] Figure 68 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00109] Figure 69 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00110] Figure 70 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00111] Figure 71 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00112] Figure 72 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00113] Figure 73 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00114] Figure 74 Exemplary Structures of hybrid type glycans and their fragments.
[00115] Figure 75A and 75B: FIG.75A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.75B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00116] Figure 76 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00117] Figure 77 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00118] Figure 78 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00119] Figure 79 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00120] Figure 80 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00121] Figure 81 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00122] Figure 82A, 82B, 82C, and 82D: FIG.82A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.82B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.82C: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.82D: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00123] Figure 83 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00124] Figure 84 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00125] Figure 85 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00126] Figure 86 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00127] Figure 87 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00128] Figure 88 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00129] Figure 89A and 89B: FIG.89A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.89B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00130] Figure 90 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. [00131] Figure 91 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00132] Figure 92 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00133] Figure 93A, 93B, and 93C: FIG.93A: Exemplary Structures of complex type glycans. FIG.93B: Exemplary Structures of complex type glycans. FIG.93C: Exemplary Structures of complex type glycans.
[00134] Figure 94 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00135] Figure 95 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00136] Figure 96 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00137] Figure 97 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00138] Figure 98 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00139] Figure 99 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00140] Figure 100 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00141] Figure 101 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00142] Figure 102A and 102B: FIG.102A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.102B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. [00143] Figure 103 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00144] Figure 104 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00145] Figure 105 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00146] Figure 106 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00147] Figure 107 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00148] Figure 108 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00149] Figure 109 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00150] Figure 110 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00151] Figure 111 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00152] Figure 112 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00153] Figure 113 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00154] Figure 114 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00155] Figure 115 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. [00156] Figure 116 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00157] Figure 117 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00158] Figure 118A, 118B, and 118C: FIG.118AExemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.118B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG.118C: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00159] Figure 119 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00160] Figure 120 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00161] Figure 121 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00162] Figure 122 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00163] Figure 123 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00164] Figure 124 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00165] Figure 125 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00166] Figure 126 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00167] Figure 127 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00168] Figure 128 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00169] Figure 129 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00170] Figure 130 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00171] Figure 131 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00172] Figure 132 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00173] Figure 134 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00174] Figure 135 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00175] Figure 136 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00176] Figure 137 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00177] Figure 138 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00178] Figure 139 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00179] Figure 140 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00180] Figure 141 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00181] Figure 142 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00182] Figure 143 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00183] Figure 144 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00184] Figure 145 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00185] Figure 146 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00186] Figure 147 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00187] Figure 148 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00188] Figure 149 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00189] Figure 150 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00190] Figure 151 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00191] Figure 152 Scheme S23 | Exemplary Preparation scheme of linear modules. [00192] Figure 153 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00193] Figure 154 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00194] Figure 155 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00195] Figure 156 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00196] Figure 157 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00197] Figure 158 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00198] Figure 159 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00199] Figure 160 Scheme S24 | Exemplary Preparation scheme of symmetrically branched modules.
[00200] Figure 161 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00201] Figure 162 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00202] Figure 163 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00203] Figure 164 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00204] Figure 165 Scheme S25 | Exemplary Preparation scheme of assymetric module. [00205] Figure 166 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00206] Figure 167 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00207] Figure 168 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00208] Figure 169 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00209] Figure 170 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00210] Figure 171 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00211] Figure 172 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00212] Figure 173 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00213] Figure 174 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00214] Figure 175 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00215] Figure 176 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00216] Figure 177 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00217] Figure 178 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. [00218] Figure 179 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00219] Figure 180 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00220] Figure 181 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00221] Figure 182 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00222] Figure 183A and 183B: FIG. 183A: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure. FIG. 183B: Exemplary structure embodiments in representative synthetic scheme embodiments of the present disclosure.
[00223] Figure 184 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00224] Figure 185 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00225] Figure 186 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00226] Figure 187 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00227] Figure 188 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00228] Figure 189 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure.
[00229] Figure 190 Exemplary structure embodiments and synthetic scheme embodiments of the present disclosure. [00230] Figure 191 Figure S4 | Schematic drawing of the fabrication of anodized aluminum oxide (AAO) glass substrate.
[00231] Figure 192 Figure S5 | FIG. 192A) AFM picture– Roughness Analysis of the surface. Img. Rms (Rq) 2.319 nm and FIG. 192B) Cross Section SEM picture of the AAO Glass Substrate.
[00232] Figure 193 Figure S6 | Structures of Cy5-phosphonic acid linker and Cy5-amine linker.
[00233] Figure 194 Figure S8 | Representative Confocal Microscopes pictures Cy5- phosphonic Acid, and Cy5-Amine on AAO glass substrate and NHS glass slide. Selective 900 μm2 area within the spots
[00234] Figure 195A, 195B, and 195C. Figure S7 | GenePix Scanning (at PMT 450) of 1 mM of (FIG. 195A) Cy5-phosphonic Acid on AAO glass substrate (FIG. 195B) Cy5-Amine on NHS glass slide, and (FIG.195C) their averaged 20 spots.
[00235] Figure 196 Figure S9 | Confocal Microscope of ConA488/Mannose binding on AAO glass Substrate vs. NHS-Glass Slide.
[00236] Figure 197A and 197B Figure S10 | Atomic force microscopy image showing sugar distribution on FIG. 197A) aluminum-oxide coated glass slide, and FIG. 197B) NHS coated glass slide
[00237] Figure 198 Figure S11 | Schematic representation of N-glycans printed on NHS coated glass slide.
[00238] Figure 199 Figure S12. Binding behavior of PG16 using NHS-coated glass slide. Bindings of PG16 to panel of N-glycans represented in bar chart.
[00239] Figure 200 Figure S17. Cartoon represents glycans printed on ACG array. The structure of linker is shown on the upper left corner.
[00240] Figure 201A and 201B (Figure S18). Bindings of PGTs 141-144 towards panel of N-glycans on ACG array is shown in bar chart. [00241] Figure 202A and 202B (Figure S19). Antibody PG16 binding curves observed for glycans X, XI and mixtures V+XI and X+XII at 100 µM concentration. The curves were obtained by using DyLight649-conjugated donkey anti-Human IgG secondary antibody.
DETAILED DESCRIPTION OF THE INVENTION
[00242] In the following description, reference is made to the accompanying drawings that form a part hereof, and in which is shown by way of illustration specific embodiments which may be practiced. These embodiments are described in detail to enable those skilled in the art to practice the invention, and it is to be understood that other embodiments may be utilized and that structural, logical and electrical changes may be made without departing from the scope of the present invention. The following description of example embodiments is, therefore, not to be taken in a limited sense, and the scope of the present invention is defined by the appended claims.
[00243] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications and patents specifically mentioned herein are incorporated by reference for all purposes including describing and disclosing the chemicals, cell lines, vectors, animals, instruments, statistical analysis and methodologies which are reported in the publications which might be used in connection with the invention. All references cited in this specification are to be taken as indicative of the level of skill in the art. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
[00244] Before the present materials and methods are described, it is understood that this invention is not limited to the particular methodology, protocols, materials, and reagents described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.
[00245] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
[00246] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989); DNA
Cloning, Volumes I and II (D. N. Glover ed., 1985); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology
(Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols.154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Antibodies: A Laboratory Manual, by Harlow and Lanes (Cold Spring Harbor Laboratory Press, 1988); and Handbook Of
Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986). Chemical definitions
[00247] Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Thomas Sorrell, Organic Chemistry, University Science Books, Sausalito, 1999; Smith and March, March’s Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3rd Edition, Cambridge University Press, Cambridge, 1987.
[00248] Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al.,
Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistry of Carbon Compounds (McGraw– Hill, NY, 1962); and Wilen, Tables of Resolving Agents and Optical Resolutions p.268 (E.L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, IN 1972). The present disclosure additionally encompasses compounds described herein as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers. [00249] When a range of values is listed, it is intended to encompass each value and sub– range within the range. For example“C1–6” is intended to encompass C1, C2, C3, C4, C5, C6, C1–6, C1–5, C1–4, C1–3, C1–2, C2–6, C2–5, C2–4, C2–3, C3–6, C3–5, C3–4, C4–6, C4–5, and C5–6.
[00250]“Alkyl” refers to a radical of a straight–chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C1–20 alkyl”). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C1–10 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C1–9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1–8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C1–7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C1–6 alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C1–5 alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C1–4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C1–3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C1–2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2–6 alkyl”).
Examples of C1–6 alkyl groups include methyl (C1), ethyl (C2), n-propyl (C3), iso-propyl (C3), n-butyl (C4), tert-butyl (C4), sec-butyl (C4), iso-butyl (C4), n-pentyl (C5), 3–pentanyl (C5), amyl (C5), neopentyl (C5), 3–methyl–2–butanyl (C5), tertiary amyl (C5), and n-hexyl (C6). Additional examples of alkyl groups include n-heptyl (C7), n-octyl (C8) and the like. Unless otherwise specified, each instance of an alkyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkyl”) or substituted (a“substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is unsubstituted C1–10 alkyl (e.g.,– CH3). In certain embodiments, the alkyl group is substituted C1–10 alkyl.
[00251]“Alkenyl” refers to a radical of a straight–chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon–carbon double bonds, and no triple bonds (“C2–20 alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C2–10 alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C2–9 alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C2–8 alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C2–7 alkenyl”). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (“C2–6 alkenyl”). In some
embodiments, an alkenyl group has 2 to 5 carbon atoms (“C2–5 alkenyl”). In some
embodiments, an alkenyl group has 2 to 4 carbon atoms (“C2–4 alkenyl”). In some
embodiments, an alkenyl group has 2 to 3 carbon atoms (“C2–3 alkenyl”). In some
embodiments, an alkenyl group has 2 carbon atoms (“C2 alkenyl”). The one or more carbon– carbon double bonds can be internal (such as in 2–butenyl) or terminal (such as in 1–butenyl). Examples of C2–4 alkenyl groups include ethenyl (C2), 1–propenyl (C3), 2–propenyl (C3), 1– butenyl (C4), 2–butenyl (C4), butadienyl (C4), and the like. Examples of C2–6 alkenyl groups include the aforementioned C2–4 alkenyl groups as well as pentenyl (C5), pentadienyl (C5), hexenyl (C6), and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (C8), octatrienyl (C8), and the like. Unless otherwise specified, each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certain
embodiments, the alkenyl group is unsubstituted C2–10 alkenyl. In certain embodiments, the alkenyl group is substituted C2–10 alkenyl.
[00252]“Alkynyl” refers to a radical of a straight–chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon–carbon triple bonds, and optionally one or more double bonds (“C2–20 alkynyl”). In some embodiments, an alkynyl group has 2 to 10 carbon atoms (“C2–10 alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (“C2–9 alkynyl”). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (“C2–8 alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C2–7 alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C2–6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C2–5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C2–4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C2–3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C2 alkynyl”). The one or more carbon– carbon triple bonds can be internal (such as in 2–butynyl) or terminal (such as in 1–butynyl). Examples of C2–4 alkynyl groups include, without limitation, ethynyl (C2), 1–propynyl (C3), 2–propynyl (C3), 1–butynyl (C4), 2–butynyl (C4), and the like. Examples of C2–6 alkenyl groups include the aforementioned C2–4 alkynyl groups as well as pentynyl (C5), hexynyl (C6), and the like. Additional examples of alkynyl include heptynyl (C7), octynyl (C8), and the like. Unless otherwise specified, each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is unsubstituted C2–10 alkynyl. In certain embodiments, the alkynyl group is substituted C2–10 alkynyl.
[00253]“Carbocyclyl” or“carbocyclic” refers to a radical of a non–aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C3–10 carbocyclyl”) and zero heteroatoms in the non–aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (“C3–8 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C3–6 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C3–6 carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (“C5–10 carbocyclyl”). Exemplary C3–6 carbocyclyl groups include, without limitation, cyclopropyl (C3), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like. Exemplary C3–8 carbocyclyl groups include, without limitation, the aforementioned C3–6 carbocyclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C7), cycloheptatrienyl (C7), cyclooctyl (C8), cyclooctenyl (C8), ydroxy[2.2.1]heptanyl (C7), ydroxy[2.2.2]octanyl (C8), and the like. Exemplary C3–10 carbocyclyl groups include, without limitation, the aforementioned C3–8 carbocyclyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro–1H–indenyl (C9), decahydronaphthalenyl (C10), spiro[4.5]decanyl (C10), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated.“Carbocyclyl” also includes ring systems wherein the carbocyclic ring, as defined above, is fused to one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclic ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted carbocyclyl”) or substituted (a“substituted carbocyclyl”) with one or more substituents. In certain embodiments, the carbocyclyl group is unsubstituted C3–10 carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C3–10 carbocyclyl.
[00254] In some embodiments,“carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C3–10 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C3–8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C3–6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C5–6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C5–10 cycloalkyl”). Examples of C5–6 cycloalkyl groups include cyclopentyl (C5) and cyclohexyl (C5). Examples of C3–6 cycloalkyl groups include the aforementioned C5–6 cycloalkyl groups as well as cyclopropyl (C3) and cyclobutyl (C4). Examples of C3–8 cycloalkyl groups include the aforementioned C3–6 cycloalkyl groups as well as cycloheptyl (C7) and cyclooctyl (C8). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an“unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certain embodiments, the cycloalkyl group is unsubstituted C3–10 cycloalkyl. In certain embodiments, the cycloalkyl group is substituted C3–10 cycloalkyl.
[00255]“Heterocyclyl” or“heterocyclic” refers to a radical of a 3– to 10–membered non– aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3–10 membered heterocyclyl”). In certain embodiments, the heteroatom is independently selected from nitrogen, sulfur, and oxygen. In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or partially unsaturated. Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system. Unless otherwise specified, each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an“unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is unsubstituted 3–10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3–10 membered heterocyclyl.
[00256] In some embodiments, a heterocyclyl group is a 5–10 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5–10 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5–8 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–8 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5–6 membered non–aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–6 membered heterocyclyl”). In some embodiments, the 5–6 membered heterocyclyl has 1–3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5–6 membered heterocyclyl has 1–2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5–6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.
[00257] Exemplary 3–membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, and thiorenyl. Exemplary 4–membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl, and thietanyl. Exemplary 5–membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl,
dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl–2,5–dione. Exemplary 5– membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5–membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6–membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6–membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplary 6– membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl. Exemplary 7–membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl, and thiepanyl. Exemplary 8–membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl, and thiocanyl. Exemplary 5-membered heterocyclyl groups fused to a C6 aryl ring (also referred to herein as a 5,6-bicyclic heterocyclic ring) include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groups fused to an aryl ring (also referred to herein as a 6,6-bicyclic heterocyclic ring) include, without limitation, tetrahydroquinolinyl,
tetrahydroisoquinolinyl, and the like.
[00258]“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having 6–14 ring carbon atoms and zero heteroatoms in the aromatic ring system (“C6–14 aryl”). In some embodiments, an aryl group has six ring carbon atoms (“C6 aryl”; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms (“C10 aryl”; e.g., naphthyl such as 1–naphthyl and 2–naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms (“C14 aryl”; e.g., anthracyl).“Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is unsubstituted C6–14 aryl. In certain embodiments, the aryl group is substituted C6–14 aryl.
[00259]“Arylalkyl” is a subset of alkyl and aryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group. In certain embodiments, the aralkyl is optionally substituted benzyl. In certain embodiments, the aralkyl is benzyl. In certain embodiments, the aralkyl is optionally substituted phenethyl. In certain embodiments, the aralkyl is phenethyl. [00260]“Heteroaryl” refers to a radical of a 5–10 membered monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 π electrons shared in a cyclic array) having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–10 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings.“Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system.“Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system. Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2–indolyl) or the ring that does not contain a heteroatom (e.g., 5– indolyl).
[00261] In some embodiments, a heteroaryl group is a 5–10 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–10 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5–8 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5–6 membered aromatic ring system having ring carbon atoms and 1–4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5–6 membered heteroaryl”). In some embodiments, the 5–6 membered heteroaryl has 1–3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5–6 membered heteroaryl has 1–2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5–6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a“substituted heteroaryl”) with one or more substituents. In certain embodiments, the heteroaryl group is unsubstituted 5–14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5–14 membered heteroaryl.
[00262] Exemplary 5–membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5–membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5–membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5–membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl. Exemplary 6–membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl. Exemplary 6–membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6–membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7–membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6–bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6– bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
[00263]“Heteroaralkyl” is a subset of alkyl and heteroaryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.
[00264] Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, which are divalent bridging groups are further referred to using the suffix– ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.
[00265] As used herein, the term“optionally substituted” refers to a substituted or unsubstituted moiety.
[00266] Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are optionally substituted (e.g.,“substituted” or“unsubstituted” alkyl, “substituted” or“unsubstituted” alkenyl,“substituted” or“unsubstituted” alkynyl, “substituted” or“unsubstituted” carbocyclyl,“substituted” or“unsubstituted” heterocyclyl, “substituted” or“unsubstituted” aryl or“substituted” or“unsubstituted” heteroaryl group). In general, the term“substituted”, whether preceded by the term“optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term“substituted” is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present present disclosure contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this present disclosure, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
[00267] Exemplary carbon atom substituents include, but are not limited to, halogen,–CN,– NO2,–N3,–SO2H,–SO3H,–OH,–ORaa,–ON(Rbb)2,–N(Rbb)2,–N(Rbb)3 +X–,–N(ORcc)Rbb,– SH,–SRaa,–SSRcc,–C(=O)Raa,–CO2H,–CHO,–C(ORcc)2,–CO2Raa,–OC(=O)Raa,– OCO2Raa,–C(=O)N(Rbb)2,–OC(=O)N(Rbb)2,–NRbbC(=O)Raa,–NRbbCO2Raa,–
NRbbC(=O)N(Rbb)2,–C(=NRbb)Raa,–C(=NRbb)ORaa,–OC(=NRbb)Raa,–OC(=NRbb)ORaa,– C(=NRbb)N(Rbb)2,–OC(=NRbb)N(Rbb)2,–NRbbC(=NRbb)N(Rbb)2,–C(=O)NRbbSO2Raa,– NRbbSO2Raa,–SO2N(Rbb)2,–SO2Raa,–SO2ORaa,–OSO2Raa,–S(=O)Raa,–OS(=O)Raa,– Si(Raa)3,–Osi(Raa)3–C(=S)N(Rbb)2,–C(=O)SRaa,–C(=S)SRaa,–SC(=S)SRaa,–SC(=O)SRaa,– OC(=O)SRaa,–SC(=O)ORaa,–SC(=O)Raa,–P(=O)2Raa,–OP(=O)2Raa,–P(=O)(Raa)2,– OP(=O)(Raa)2,–OP(=O)(ORcc)2,–P(=O)2N(Rbb)2,–OP(=O)2N(Rbb)2,–P(=O)(NRbb)2,– OP(=O)(NRbb)2,–NRbbP(=O)(ORcc)2,–NRbbP(=O)(NRbb)2,–P(Rcc)2,–P(Rcc)3,–OP(Rcc)2,– OP(Rcc)3,–B(Raa)2,–B(ORcc)2,–BRaa(ORcc), C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
or two hydrogens on a carbon atom are replaced with the group =O, =S, =NN(Rbb)2, =NNRbbC(=O)Raa, =NNRbbC(=O)ORaa, =NNRbbS(=O)2Raa, =NRbb, or =NORcc;
each instance of Raa is, independently, selected from C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two Raa groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
each instance of Rbb is, independently, selected from hydrogen,–OH,–ORaa,– N(Rcc)2,–CN,–C(=O)Raa,–C(=O)N(Rcc)2,–CO2Raa,–SO2Raa,–C(=NRcc)ORaa,–
C(=NRcc)N(Rcc)2,–SO2N(Rcc)2,–SO2Rcc,–SO2ORcc,–SORaa,–C(=S)N(Rcc)2,–C(=O)SRcc,– C(=S)SRcc,–P(=O)2Raa,–P(=O)(Raa)2,–P(=O)2N(Rcc)2,–P(=O)(NRcc)2, C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two Rbb groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
each instance of Rcc is, independently, selected from hydrogen, C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two Rcc groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
each instance of Rdd is, independently, selected from halogen,–CN,–NO2,–N3,– SO2H,–SO3H,–OH,–ORee,–ON(Rff)2,–N(Rff)2,–N(Rff)3+X–,–N(ORee)Rff,–SH,–SRee,– SSRee,–C(=O)Ree,–CO2H,–CO2Ree,–OC(=O)Ree,–OCO2Ree,–C(=O)N(Rff)2,–
OC(=O)N(Rff)2,–NRffC(=O)Ree,–NRffCO2Ree,–NRffC(=O)N(Rff)2,–C(=NRff)ORee,– OC(=NRff)Ree,–OC(=NRff)ORee,–C(=NRff)N(Rff)2,–OC(=NRff)N(Rff)2,–
NRffC(=NRff)N(Rff)2,–NRffSO2Ree,–SO2N(Rff)2,–SO2Ree,–SO2ORee,–OSO2Ree,–S(=O)Ree, –Si(Ree)3,–Osi(Ree)3,–C(=S)N(Rff)2,–C(=O)SRee,–C(=S)SRee,–SC(=S)SRee,–P(=O)2Ree,– P(=O)(Ree)2,–OP(=O)(Ree)2,–OP(=O)(ORee)2, C1–6 alkyl, C1–6 perhaloalkyl, C2–6 alkenyl, C2– 6 alkynyl, C3–10 carbocyclyl, 3–10 membered heterocyclyl, C6–10 aryl, 5–10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups, or two Rdd substituents can be joined to form =O or =S;
each instance of Ree is, independently, selected from C1–6 alkyl, C1–6 perhaloalkyl, C2– 6 alkenyl, C2–6 alkynyl, C3–10 carbocyclyl, C6–10 aryl, 3–10 membered heterocyclyl, and 3–10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups;
each instance of Rff is, independently, selected from hydrogen, C1–6 alkyl, C1–6 perhaloalkyl, C2–6 alkenyl, C2–6 alkynyl, C3–10 carbocyclyl, 3–10 membered heterocyclyl, C6– 10 aryl and 5–10 membered heteroaryl, or two Rff groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; and
each instance of Rgg is, independently, halogen,–CN,–NO2,–N3,–SO2H,–SO3H,– OH,–OC1–6 alkyl,–ON(C1–6 alkyl)2,–N(C1–6 alkyl)2,–N(C1–6 alkyl)3 +X–,–NH(C1–6 alkyl)2+X–,–NH2(C1–6 alkyl) +X–,–NH3+X–,–N(OC1–6 alkyl)(C1–6 alkyl),–N(OH)(C1–6 alkyl), –NH(OH),–SH,–SC1–6 alkyl,–SS(C1–6 alkyl),–C(=O)(C1–6 alkyl),–CO2H,–CO2(C1–6 alkyl),–OC(=O)(C1–6 alkyl),–OCO2(C1–6 alkyl),–C(=O)NH2,–C(=O)N(C1–6 alkyl)2,– OC(=O)NH(C1–6 alkyl),–NHC(=O)( C1–6 alkyl),–N(C1–6 alkyl)C(=O)( C1–6 alkyl),– NHCO2(C1–6 alkyl),–NHC(=O)N(C1–6 alkyl)2,–NHC(=O)NH(C1–6 alkyl),–NHC(=O)NH2,– C(=NH)O(C1–6 alkyl),–OC(=NH)(C1–6 alkyl),–OC(=NH)OC1–6 alkyl,–C(=NH)N(C1–6 alkyl)2,–C(=NH)NH(C1–6 alkyl),–C(=NH)NH2,–OC(=NH)N(C1–6 alkyl)2,–OC(NH)NH(C1– 6 alkyl),–OC(NH)NH2,–NHC(NH)N(C1–6 alkyl)2,–NHC(=NH)NH2,–NHSO2(C1–6 alkyl),– SO2N(C1–6 alkyl)2,–SO2NH(C1–6 alkyl),–SO2NH2,–SO2C1–6 alkyl,–SO2OC1–6 alkyl,– OSO2C1–6 alkyl,–SOC1–6 alkyl,–Si(C1–6 alkyl)3,–Osi(C1–6 alkyl)3–C(=S)N(C1–6 alkyl)2, C(=S)NH(C1–6 alkyl), C(=S)NH2,–C(=O)S(C1–6 alkyl),–C(=S)SC1–6 alkyl,–SC(=S)SC1–6 alkyl,–P(=O)2(C1–6 alkyl),–P(=O)(C1–6 alkyl)2,–OP(=O)(C1–6 alkyl)2,–OP(=O)(OC1–6 alkyl)2, C1–6 alkyl, C1–6 perhaloalkyl, C2–6 alkenyl, C2–6 alkynyl, C3–10 carbocyclyl, C6–10 aryl, 3–10 membered heterocyclyl, 5–10 membered heteroaryl; or two Rgg substituents can be joined to form =O or =S; wherein X– is a counterion.
[00268]“Halo” or“halogen” refers to fluorine (fluoro,–F), chlorine (chloro,–Cl), bromine (bromo,–Br), or iodine (iodo,–I).
[00269]“Acyl” as used herein refers to a moiety selected from the group consisting of– C(=O)Raa,–CHO,–CO2Raa,–C(=O)N(Rbb)2,–C(=NRbb)Raa,–C(=NRbb)ORaa,–
C(=NRbb)N(Rbb)2,–C(=O)NRbbSO2Raa,–C(=S)N(Rbb)2,–C(=O)SRaa, and–C(=S)SRaa, wherein Raa and Rbb are as defined herein.
[00270] Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary nitrogen atom substituents include, but are not limited to, hydrogen,–OH,–ORaa,–N(Rcc)2,–CN,– C(=O)Raa,–C(=O)N(Rcc)2,–CO2Raa,–SO2Raa,–C(=NRbb)Raa,–C(=NRcc)ORaa,–
C(=NRcc)N(Rcc)2,–SO2N(Rcc)2,–SO2Rcc,–SO2ORcc,–SORaa,–C(=S)N(Rcc)2,–C(=O)SRcc,– C(=S)SRcc,–P(=O)2Raa,–P(=O)(Raa)2,–P(=O)2N(Rcc)2,–P(=O)(NRcc)2, C1–10 alkyl, C1–10 perhaloalkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl, or two Rcc groups attached to a nitrogen atom are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc, and Rdd are as defined above.
[00271] In certain embodiments, the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group). Nitrogen protecting groups include, but are not limited to,–OH,–ORaa,–N(Rcc)2,–C(=O)Raa,–C(=O)N(Rcc)2,–CO2Raa, –SO2Raa,–C(=NRcc)Raa,–C(=NRcc)ORaa,–C(=NRcc)N(Rcc)2,–SO2N(Rcc)2,–SO2Rcc,– SO2ORcc,–SORaa,–C(=S)N(Rcc)2,–C(=O)SRcc,–C(=S)SRcc, C1–10 alkyl (e.g., aralkyl, heteroaralkyl), C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc and Rdd are as defined herein. Nitrogen protecting groups are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
[00272] For example, nitrogen protecting groups such as amide groups (e.g.,–C(=O)Raa) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3–phenylpropanamide, picolinamide, 3–
pyridylcarboxamide, N–benzoylphenylalanyl derivative, benzamide, p–phenylbenzamide, o– nitophenylacetamide, o–nitrophenoxyacetamide, acetoacetamide, (N ^–
dithiobenzyloxyacylamino)acetamide, 3–(p–hydroxyphenyl)propanamide, 3–(o–
nitrophenyl)propanamide, 2–methyl–2–(o–nitrophenoxy)propanamide, 2–methyl–2–(o– phenylazophenoxy)propanamide, 4–chlorobutanamide, 3–methyl–3–nitrobutanamide, o– nitrocinnamide, N–acetylmethionine derivative, o–nitrobenzamide, and o–
(benzoyloxymethyl)benzamide.
[00273] Nitrogen protecting groups such as carbamate groups (e.g.,–C(=O)ORaa) include, but are not limited to, methyl carbamate, ethyl carbamante, 9–fluorenylmethyl carbamate (Fmoc), 9–(2–sulfo)fluorenylmethyl carbamate, 9–(2,7–dibromo)fluoroenylmethyl carbamate, 2,7–di–t–butyl–[9–(10,10–dioxo–10,10,10,10–tetrahydrothioxanthyl)]methyl carbamate (DBD–Tmoc), 4–methoxyphenacyl carbamate (Phenoc), 2,2,2–trichloroethyl carbamate (Troc), 2–trimethylsilylethyl carbamate (Teoc), 2–phenylethyl carbamate (hZ), 1- (1-Adamantyl)-1-methylethyl (Adpoc), 1,1–dimethyl–2–haloethyl carbamate, 1,1–dimethyl– 2,2–dibromoethyl carbamate (DB–t–BOC), 1,1–dimethyl–2,2,2–trichloroethyl carbamate (TCBOC), 1–methyl–1–(4–biphenylyl)ethyl carbamate (Bpoc), 1–(3,5–di–t–butylphenyl)–1– methylethyl carbamate (t–Bumeoc), 2–(2 ^– and 4 ^–pyridyl)ethyl carbamate (Pyoc), 2–(N,N– dicyclohexylcarboxamido)ethyl carbamate, t–butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1–isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4–nitrocinnamyl carbamate (Noc), 8–quinolyl carbamate, N– hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p– methoxybenzyl carbamate (Moz), p–nitobenzyl carbamate, p–bromobenzyl carbamate, p– chlorobenzyl carbamate, 2,4–dichlorobenzyl carbamate, 4–methylsulfinylbenzyl carbamate (Msz), 9–anthrylmethyl carbamate, diphenylmethyl carbamate, 2–methylthioethyl carbamate, 2–methylsulfonylethyl carbamate, 2–(p–toluenesulfonyl)ethyl carbamate, [2–(1,3– dithianyl)]methyl carbamate (Dmoc), 4–methylthiophenyl carbamate (Mtpc), 2,4– dimethylthiophenyl carbamate (Bmpc), 2–phosphonioethyl carbamate (Peoc), 2–
triphenylphosphonioisopropyl carbamate (Ppoc), 1,1–dimethyl–2–cyanoethyl carbamate, m– chloro–p–acyloxybenzyl carbamate, p–(dihydroxyboryl)benzyl carbamate, 5–
benzisoxazolylmethyl carbamate, 2–(trifluoromethyl)–6–chromonylmethyl carbamate (Tcroc), m–nitrophenyl carbamate, 3,5–dimethoxybenzyl carbamate, o–nitrobenzyl carbamate, 3,4–dimethoxy–6–nitrobenzyl carbamate, phenyl(o–nitrophenyl)methyl carbamate, t–amyl carbamate, S–benzyl thiocarbamate, p–cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p– decyloxybenzyl carbamate, 2,2–dimethoxyacylvinyl carbamate, o–(N,N–
dimethylcarboxamido)benzyl carbamate, 1,1–dimethyl–3–(N,N–dimethylcarboxamido)propyl carbamate, 1,1–dimethylpropynyl carbamate, di(2–pyridyl)methyl carbamate, 2–
furanylmethyl carbamate, 2–iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p–(p ^–methoxyphenylazo)benzyl carbamate, 1–methylcyclobutyl carbamate, 1–methylcyclohexyl carbamate, 1–methyl–1–cyclopropylmethyl carbamate, 1– methyl–1–(3,5–dimethoxyphenyl)ethyl carbamate, 1–methyl–1–(p–phenylazophenyl)ethyl carbamate, 1–methyl–1–phenylethyl carbamate, 1–methyl–1–(4–pyridyl)ethyl carbamate, phenyl carbamate, p–(phenylazo)benzyl carbamate, 2,4,6–tri–t–butylphenyl carbamate, 4– (trimethylammonium)benzyl carbamate, and 2,4,6–trimethylbenzyl carbamate.
[00274] Nitrogen protecting groups such as sulfonamide groups (e.g.,–S(=O)2Raa) include, but are not limited to, p–toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,–trimethyl–4– methoxybenzenesulfonamide (Mtr), 2,4,6–trimethoxybenzenesulfonamide (Mtb), 2,6– dimethyl–4–methoxybenzenesulfonamide (Pme), 2,3,5,6–tetramethyl–4–
methoxybenzenesulfonamide (Mte), 4–methoxybenzenesulfonamide (Mbs), 2,4,6– trimethylbenzenesulfonamide (Mts), 2,6–dimethoxy–4–methylbenzenesulfonamide (iMds), 2,2,5,7,8–pentamethylchroman–6–sulfonamide (Pmc), methanesulfonamide (Ms), β– trimethylsilylethanesulfonamide (SES), 9–anthracenesulfonamide, 4–(4 ^,8 ^–
dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide,
trifluoromethylsulfonamide, and phenacylsulfonamide.
[00275] Other nitrogen protecting groups include, but are not limited to, phenothiazinyl– (10)–acyl derivative, N ^–p–toluenesulfonylaminoacyl derivative, N ^–phenylaminothioacyl derivative, N–benzoylphenylalanyl derivative, N–acetylmethionine derivative, 4,5–diphenyl– 3–oxazolin–2–one, N–phthalimide, N–dithiasuccinimide (Dts), N–2,3–diphenylmaleimide, N–2,5–dimethylpyrrole, N–1,1,4,4–tetramethyldisilylazacyclopentane adduct (STABASE), 5–substituted 1,3–dimethyl–1,3,5–triazacyclohexan–2–one, 5–substituted 1,3–dibenzyl– 1,3,5–triazacyclohexan–2–one, 1–substituted 3,5–dinitro–4–hydroxyl, N–methylamine, N– allylamine, N–[2–(trimethylsilyl)ethoxy]methylamine (SEM), N–3–acetoxypropylamine, N– (1–isopropyl–4–nitro–2–oxo–3–pyroolin–3–yl)amine, quaternary ammonium salts, N– benzylamine, N–di(4–methoxyphenyl)methylamine, N–5–dibenzosuberylamine, N– triphenylmethylamine (Tr), N–[(4–methoxyphenyl)diphenylmethyl]amine (MMTr), N–9– phenylfluorenylamine (PhF), N–2,7–dichloro–9–fluorenylmethyleneamine, N–
ferrocenylmethylamino (Fcm), N–2–picolylamino N ^–oxide, N–1,1–
dimethylthiomethyleneamine, N–benzylideneamine, N–p–methoxybenzylideneamine, N– diphenylmethyleneamine, N–[(2–pyridyl)mesityl]methyleneamine, N–(N ^,N ^– dimethylaminomethylene)amine, N,N ^–isopropylidenediamine, N–p–nitrobenzylideneamine, N–salicylideneamine, N–5–chlorosalicylideneamine, N–(5–chloro–2–
hydroxyphenyl)phenylmethyleneamine, N–cyclohexylideneamine, N–(5,5–dimethyl–3–oxo– 1–cyclohexenyl)amine, N–borane derivative, N–diphenylborinic acid derivative, N–
[phenyl(pentaacylchromium– or tungsten)acyl]amine, N–copper chelate, N–zinc chelate, N– nitroamine, N–nitrosoamine, amine N–oxide, diphenylphosphinamide (Dpp),
dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl
phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate,
benzenesulfenamide, o–nitrobenzenesulfenamide (Nps), 2,4–dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2–nitro–4–methoxybenzenesulfenamide,
triphenylmethylsulfenamide, and 3–nitropyridinesulfenamide (Npys).
[00276] In certain embodiments, the substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group). Oxygen protecting groups include, but are not limited to,–Raa,–N(Rbb)2,–C(=O)SRaa,–C(=O)Raa,–CO2Raa,–
C(=O)N(Rbb)2,–C(=NRbb)Raa,–C(=NRbb)ORaa,–C(=NRbb)N(Rbb)2,–S(=O)Raa,–SO2Raa,– Si(Raa)3,–P(Rcc)2,–P(Rcc)3,–P(=O)2Raa,–P(=O)(Raa)2,–P(=O)(ORcc)2,–P(=O)2N(Rbb)2, and– P(=O)(NRbb)2, wherein Raa, Rbb, and Rcc are as defined herein. Oxygen protecting groups are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
[00277] Exemplary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t–butylthiomethyl,
(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p–
methoxybenzyloxymethyl (PMBM), (4–methoxyphenoxy)methyl (p–AOM), guaiacolmethyl (GUM), t–butoxymethyl, 4–pentenyloxymethyl (POM), siloxymethyl, 2– methoxyethoxymethyl (MEM), 2,2,2–trichloroethoxymethyl, bis(2–chloroethoxy)methyl, 2– (trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3–
bromotetrahydropyranyl, tetrahydrothiopyranyl, 1–methoxycyclohexyl, 4–
methoxytetrahydropyranyl (MTHP), 4–methoxytetrahydrothiopyranyl, 4–
methoxytetrahydrothiopyranyl S,S–dioxide, 1–[(2–chloro–4–methyl)phenyl]–4–
methoxypiperidin–4–yl (CTMP), 1,4–dioxan–2–yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a–octahydro–7,8,8–trimethyl–4,7–methanobenzofuran–2–yl, 1–ethoxyethyl, 1–(2–chloroethoxy)ethyl, 1–methyl–1–methoxyethyl, 1–methyl–1–benzyloxyethyl, 1– methyl–1–benzyloxy–2–fluoroethyl, 2,2,2–trichloroethyl, 2–trimethylsilylethyl, 2–
(phenylselenyl)ethyl, t–butyl, allyl, p–chlorophenyl, p–methoxyphenyl, 2,4–dinitrophenyl, benzyl (Bn), p–methoxybenzyl, 3,4–dimethoxybenzyl, o–nitrobenzyl, p–nitrobenzyl, p– halobenzyl, 2,6–dichlorobenzyl, p–cyanobenzyl, p–phenylbenzyl, 2–picolyl, 4–picolyl, 3– methyl–2–picolyl N–oxido, diphenylmethyl, p,p’–dinitrobenzhydryl, 5–dibenzosuberyl, triphenylmethyl, α–naphthyldiphenylmethyl, p–methoxyphenyldiphenylmethyl, di(p– methoxyphenyl)phenylmethyl, tri(p–methoxyphenyl)methyl, 4–(4’–
bromophenacyloxyphenyl)diphenylmethyl, 4,4′,4″–tris(4,5–
dichlorophthalimidophenyl)methyl, 4,4′,4″–tris(levulinoyloxyphenyl)methyl, 4,4′,4″– tris(benzoyloxyphenyl)methyl, 3–(imidazol–1–yl)bis(4′,4″–dimethoxyphenyl)methyl, 1,1– bis(4–methoxyphenyl)–1′–pyrenylmethyl, 9–anthryl, 9–(9–phenyl)xanthenyl, 9–(9–phenyl– 10–oxo)anthryl, 1,3–benzodithiolan–2–yl, benzisothiazolyl S,S–dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t–butyldimethylsilyl (TBDMS), t– butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri–p–xylylsilyl, triphenylsilyl,
diphenylmethylsilyl (DPMS), t–butylmethoxyphenylsilyl (TBMPS), formate,
benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p–chlorophenoxyacetate, 3– phenylpropionate, 4–oxopentanoate (levulinate), 4,4–(ethylenedithio)pentanoate
(levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4–methoxycrotonate, benzoate, p– phenylbenzoate, 2,4,6–trimethylbenzoate (mesitoate), methyl carbonate, 9–fluorenylmethyl carbonate (Fmoc), ethyl carbonate, 2,2,2–trichloroethyl carbonate (Troc), 2–
(trimethylsilyl)ethyl carbonate (TMSEC), 2–(phenylsulfonyl) ethyl carbonate (Psec), 2– (triphenylphosphonio) ethyl carbonate (Peoc), isobutyl carbonate, vinyl carbonate, allyl carbonate, t–butyl carbonate (BOC), p–nitrophenyl carbonate, benzyl carbonate, p– methoxybenzyl carbonate, 3,4–dimethoxybenzyl carbonate, o–nitrobenzyl carbonate, p– nitrobenzyl carbonate, S–benzyl thiocarbonate, 4–ethoxy–1–napththyl carbonate, methyl dithiocarbonate, 2–iodobenzoate, 4–azidobutyrate, 4–nitro–4–methylpentanoate, o–
(dibromomethyl)benzoate, 2–formylbenzenesulfonate, 2–(methylthiomethoxy)ethyl, 4– (methylthiomethoxy)butyrate, 2–(methylthiomethoxymethyl)benzoate, 2,6–dichloro–4– methylphenoxyacetate, 2,6–dichloro–4–(1,1,3,3–tetramethylbutyl)phenoxyacetate, 2,4– bis(1,1–dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)–2–methyl–2–butenoate, o–(methoxyacyl)benzoate, α–naphthoate, nitrate, alkyl
N,N,N’,N’–tetramethylphosphorodiamidate, alkyl N–phenylcarbamate, borate,
dimethylphosphinothioyl, alkyl 2,4–dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).
[00278] In certain embodiments, the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups include, but are not limited to,–Raa,–N(Rbb)2,–C(=O)SRaa,–C(=O)Raa,–CO2Raa,–C(=O)N(Rbb)2,–
C(=NRbb)Raa,–C(=NRbb)ORaa,–C(=NRbb)N(Rbb)2,–S(=O)Raa,–SO2Raa,–Si(Raa)3,–P(Rcc)2,– P(Rcc)3,–P(=O)2Raa,–P(=O)(Raa)2,–P(=O)(ORcc)2,–P(=O)2N(Rbb)2, and–P(=O)(NRbb)2, wherein Raa, Rbb, and Rcc are as defined herein. The term“protecting groups, and in particular sulfur protecting groups, are well known in the art and include those described in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference in its entirety.
[00279] As used herein, the term“leaving group” is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. Examples of suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, and haloformates. In some cases, the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate,–OTs), methanesulfonate (mesylate,– OMs), p-bromobenzenesulfonyloxy (brosylate,–OBs), or trifluoromethanesulfonate (triflate, –OTf). In some cases, the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy. In some cases, the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy. In some embodiments, the leaving group is a sulfonate-containing group. In some embodiments, the leaving group is a tosylate group. The leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
Definitions:
[00280] As used herein, the term“glycan” refers to a polysaccharide, oligosaccharide or monosaccharide. Glycans can be monomers or polymers of sugar residues and can be linear or branched. A glycan may include natural sugar residues (e.g., glucose, N- acetylglucosamine, N-acetyl neuraminic acid, galactose, mannose, fucose, hexose, arabinose, ribose, xylose, etc.) and/or modified sugars (e.g., 2′-fluororibose, 2′-deoxyribose,
phosphomannose, 6′ sulfo N-acetylglucosamine, etc). Glycan is also used herein to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, glycopeptide, glycoproteome, peptidoglycan, lipopolysaccharide or a proteoglycan. Glycans usually consist solely of O-glycosidic linkages between monosaccharides. For example, cellulose is a glycan (or more specifically a glucan) composed of ß-1,4-linked D-glucose, and chitin is a glycan composed of ß-1,4-linked N-acetyl-D-glucosamine. Glycans can be homo or heteropolymers of monosaccharide residues, and can be linear or branched. Glycans can be found attached to proteins as in glycoproteins and proteoglycans. They are generally found on the exterior surface of cells. O- and N-linked glycans are very common in eukaryotes but may also be found, although less commonly, in prokaryotes.
[00281] As used herein, the terms“fucose”,“core fucose” and“ core fucose residue” are used interchangeably and refer to a fucose in ^1,6-position linked to the N- acetylglucosamine.
[00282] As used herein, the terms“N-glycan”,“N-linked glycan”,“N-linked glycosylation”, “Fc glycan” and“Fc glycosylation” are used interchangeably and refer to an N-linked oligosaccharide attached by an N-acetylglucosamine (GlcNAc) linked to the amide nitrogen of an asparagine residue in a Fc-containing polypeptide. The term“Fc-containing polypeptide” refers to a polypeptide, such as an antibody, which comprises an Fc region.
[00283] As used herein, the term“glycosylation pattern” and“glycosylation profile” are used interchangeably and refer to the characteristic“fingerprint” of the N-glycan species that have been released from a glycoprotein or antibody, either enzymatically or chemically, and then analyzed for their carbohydrate structure, for example, using LC-HPLC, or MALDI-TOF MS, and the like. See, for example, the review in Current Analytical Chemistry, Vol.1, No.1 (2005), pp.28-57; herein incorporated by reference in its entirety.
[00284] As used herein,“broadly neutralizing HIV-1 antibodies” are neutralizing antibodies which neutralize multiple HIV-1 viral strains and can include or exclude any one or more of the following antibody examplars:
Figure imgf000057_0001
[00285] A“defined glycan probe location” as used herein is a predefined region of a solid support to which a density of glycan molecules, all having similar glycan structures, is attached. The terms“glycan region,” or“selected region”, or simply“region” are used interchangeably herein for the term defined glycan probe location. The defined glycan probe location may have any convenient shape, for example, circular, rectangular, elliptical, wedge- shaped, and the like. In some embodiments, a defined glycan probe location and, therefore, the area upon which each distinct glycan type or a distinct group of structurally related glycans is attached is smaller than about 1 cm2, or less than 1 mm2, or less than 0.5 mm2. In some embodiments the glycan probe locations have an area less than about 10,000 μm2 or less than 100 μm2. The glycan molecules attached within each defined glycan probe location are substantially identical. Additionally, multiple copies of each glycan type are present within each defined glycan probe location. The number of copies of each glycan types within each defined glycan probe location can be in the thousands to the millions.
[00286] As used herein, the arrays of the present disclosure have defined glycan probe locations, each with“one type of glycan molecule.” The“one type of glycan molecule” employed can be a group of substantially structurally identical glycan molecules or a group of structurally similar glycan molecules. There is no need for every glycan molecule within a defined glycan probe location to have an identical structure. In some embodiments, the glycans within a single defined glycan probe location are structural isomers, have variable numbers of sugar units or are branched in somewhat different ways. However, in general, the glycans within a defined glycan probe location have substantially the same type of sugar units and/or approximately the same proportion of each type of sugar unit. The types of substituents on the sugar units of the glycans within a defined glycan probe location are also substantially the same.
[00287] Detection of binding can be direct, for example, by detection of a label directly attached to the test molecule. Alternatively, detection can be indirect, for example, by detecting a labeled secondary antibody or other labeled molecule that can bind to the test molecule. The bound label can be observed using any available detection method. For example, an array CCD analyzer can be employed to detect chemiluminescence labeled molecules that are bound to array.
[00288] As used herein, the term“antigen” is defined as any substance capable of eliciting an immune response.
[00289] As used herein, the term“immunogenicity” refers to the ability of an immunogen, antigen, or vaccine to stimulate an immune response.
[00290] As used herein, the term“epitope” is defined as the parts of an antigen molecule which contact the antigen binding site of an antibody or a T cell receptor.
[00291] As used herein, the term“vaccine” refers to a preparation that contains an antigen, consisting of whole disease-causing organisms (killed or weakened) or components of such organisms, such as proteins, peptides, or polysaccharides, that is used to confer immunity against the disease that the organisms cause. Vaccine preparations can be natural, synthetic or derived by recombinant DNA technology.
[00292] As used herein, the term“antigen specific” refers to a property of a cell population such that supply of a particular antigen, or a fragment of the antigen, results in specific cell proliferation.
[00293] As used herein, the term "specifically binding," refers to the interaction between binding pairs (e.g., an antibody and an antigen). In various instances, specifically binding can be embodied by an affinity constant of about 10-6 moles/liter, about 10-7 moles/liter, or about 10-8 moles/liter, or less.
[00294] An“isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with research, diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In one embodiment, the antibody will be purified (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of, for example, a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using, for example, Coomassie blue or silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
[00295] The term“support” or“substrate” as used interchangeably herein refers to a material or group of materials, comprising one or a plurality of components, with which one or more molecules are directly or indirectly bound, attached, synthesized upon, linked, or otherwise associated. A support may be constructed from materials that are biological, non-biological, inorganic, organic or a combination of these. A support may be in any appropriate size or configuration based upon its use within a particular embodiment.
[00296] The term“target” as used herein refers to a species of interest within an assay. Targets may be naturally occurring or synthetic, or a combination. Targets may be unaltered (e.g., utilized directly within the organism or a sample thereof), or altered in a manner appropriate for the assay (e.g., purified, amplified, filtered). Targets may be bound through a suitable means to a binding member within certain assays. Non-limiting examples of targets include, but are not restricted to, antibodies or fragments thereof, cell membrane receptors, monoclonal antibodies and antisera reactive with specific antigenic determinants (such as on viruses, cells or other materials), drugs, oligonucleotides, nucleic acids, peptides, cofactors, sugars, lectins polysaccharides, cells, cellular membranes, and organelles. Target may be any suitable size depending on the assay.
[00297] The phrase“substantially similar,”“substantially the same”,“equivalent”, or “substantially equivalent”, as used herein, denotes a sufficiently high degree of similarity between two numeric values (for example, one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values, anti-viral effects, etc.). The difference between said two values is, for example, less than about 50%, less than about 40%, less than about 30%, less than about 20%, and/or less than about 10% as a function of the value for the reference/comparator molecule.
[00298] The phrase“substantially reduced,” or“substantially different”, as used herein, denotes a sufficiently high degree of difference between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values is, for example, greater than about 10%, greater than about 20%, greater than about 30%, greater than about 40%, and/or greater than about 50% as a function of the value for the reference/comparator molecule.
[00299]“Binding affinity” generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein,“binding affinity” refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd). Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present present disclosure. Specific illustrative embodiments are described in the following. [00300]“Polynucleotide,” or“nucleic acid,” as used interchangeably herein, refer to polymers of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after synthesis, such as by conjugation with a label. Other types of modifications include, for example,“caps,” substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotides(s). Further, any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports. The 5′ and 3′ terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms. Other hydroxyls may also be derivatized to standard protecting groups. Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2′-O-methyl-, 2′-O-allyl, 2′-fluoro- or 2′-azido-ribose, carbocyclic sugar analogs, α-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and basic nucleoside analogs such as methyl riboside. One or more phosphodiester linkages may be replaced by alternative linking groups. These alternative linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(O)S (“thioate”), P(S)S (“dithioate”),“(O)NR2 (“amidate”), P(O)R, P(O)OR′, CO or CH2 (“formacetal”), in which each R or R′ is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
[00301]“Oligonucleotide,” as used herein, generally refers to short, generally single- stranded, generally synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length. The terms“oligonucleotide” and“polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
[00302]“Antibodies” (Abs) and“immunoglobulins” (IGs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which generally lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
[00303] The terms“antibody” and“immunoglobulin” are used interchangeably in the broadest sense and include monoclonal antibodies (e.g., full length or intact monoclonal antibodies), polyclonal antibodies, monovalent, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies so long as they exhibit the desired biological activity) and may also include certain antibody fragments (as described in greater detail herein). An antibody can be chimeric, human, humanized and/or affinity matured. [00304] The“variable region” or“variable domain” of an antibody refers to the amino- terminal domains of heavy or light chain of the antibody. These domains are generally the most variable parts of an antibody and contain the antigen-binding sites.
[00305] The term“variable” refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR). The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a beta-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, Md. (1991)). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.
[00306] Papain digestion of antibodies produces two identical antigen-binding fragments, called“Fab” fragments, each with a single antigen-binding site, and a residual“Fc” fragment, whose name reflects its ability to crystallize readily. Pepsin treatment yields an F(ab′)2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
[00307]“Fv” is the minimum antibody fragment which contains a complete antigen- recognition and -binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. In a single- chain Fv species, one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a“dimeric” structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
[00308] The Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain. Fab′ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab′)2 antibody fragments originally were produced as pairs of Fab′ fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
[00309] The“light chains” of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa (κ) and lambda (λ), based on the amino acid sequences of their constant domains.
[00310] Depending on the amino acid sequences of the constant domains of their heavy chains, antibodies (immunoglobulins) can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known and described generally in, for example, Abbas et al. Cellular and Mol. Immunology, 4th ed. (2000). An antibody may be part of a larger fusion molecule, formed by covalent or non-covalent association of the antibody with one or more other proteins or peptides.
[00311] The terms“full length antibody,”“intact antibody” and“whole antibody” are used herein interchangeably, to refer to an antibody in its substantially intact form, not antibody fragments as defined below. The terms particularly refer to an antibody with heavy chains that contain the Fc region.
[00312]“Antibody fragments” comprise only a portion of an intact antibody, wherein the portion retains at least one, and as many as most or all, of the functions normally associated with that portion when present in an intact antibody. In one embodiment, an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen. In another embodiment, an antibody fragment, for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half- life modulation, ADCC function and complement binding. In one embodiment, an antibody fragment is a monovalent antibody that has an in vivo half-life substantially similar to an intact antibody. For example, such an antibody fragment may comprise an antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment.
[00313] The term“monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier“monoclonal” indicates the character of the antibody as not being a mixture of discrete antibodies. Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones. It should be understood that the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this present disclosure. In contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. In addition to their specificity, the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins. The modifier“monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present disclosure may be made by a variety of techniques, including, for example, the hybridoma method (e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Pat. No.4,816,567), phage display technologies (See, e.g., Clackson et al., Nature, 352: 624-628 (1991); Marks et al., J. Mol. Biol.222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2): 299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al., J. Immunol. Methods 284(1-2): 119-132 (2004), and technologies for producing human or human-like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences (see, e.g., WO98/24893; WO96/34096; WO96/33735; WO91/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993); Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016; Marks et al., Bio. Technology 10: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild et al., Nature Biotechnol. 14: 845- 851 (1996); Neuberger, Nature Biotechnol. 14: 826 (1996) and Lonberg and Huszar, Intern. Rev. Immunol.13: 65-93 (1995).
[00314] The monoclonal antibodies herein specifically include“chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No.4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).
[00315]“Humanized” forms of non-human (e.g., murine) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin. In one embodiment, a humanized antibody is a human immunoglobulin (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the following review articles and references cited therein: Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1:105-115 (1998); Harris, Biochem. Soc. Transactions 23:1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech.5:428-433 (1994).
[00316] As used herein,“normal levels” can be, for example, a reference value or range based on measurements of the levels of TACA bound antibodies in samples from normal patients or a population of normal patients. “Normal levels” can also be, for example, a reference value or range based on measurements of the TACAs in samples from normal patients or a population of normal patients.
[00317] As used herein a“subject” is a mammal. Such mammals include domesticated animals, farm animals, animals used in experiments, zoo animals and the like. In some embodiments, the subject is a human.
[00318] A“disorder” is any condition that would benefit from treatment with an antibody of the present disclosure. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non- limiting examples of disorders to be treated herein include HIV.
[00319] The following definitions are more general terms used throughout the present application.
[00320] As used herein and in the appended claims, the singular forms "a," "and," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, "a transport enhancer" encompasses a plurality of transport enhancers as well as a single transport enhancer. Reference to "a chelating agent" includes reference to two or more chelating agents as well as a single chelating agent, and so forth. In this specification and in the claims that follow, reference will be made to a number of terms, which shall be defined to have the following meanings:
[00321] The terms "treating" and "treatment" as used herein refer to the administration of an agent or formulation to a clinically symptomatic individual afflicted with an adverse condition, disorder, or disease, so as to effect a reduction in severity and/or frequency of symptoms, eliminate the symptoms and/or their underlying cause, and/or facilitate improvement or remediation of damage. The terms "preventing" and "prevention" refer to the administration of an agent or composition to a clinically asymptomatic individual who is susceptible to a particular adverse condition, disorder, or disease, and thus relates to the prevention of the occurrence of symptoms and/or their underlying cause. Unless otherwise indicated herein, either explicitly or by implication, if the term "treatment" (or "treating") is used without reference to possible prevention, it is intended that prevention be encompassed as well.
[00322] "Optional" or "optionally present" - as in an "optional substituent" or an "optionally present additive" means that the subsequently described component (e.g., substituent or additive) may or may not be present, so that the description includes instances where the component is present and instances where it is not.
[00323] By "pharmaceutically acceptable" is meant a material that is not biologically or otherwise undesirable, e.g., the material may be incorporated into a formulation of the present disclosure without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the dosage form formulation. However, when the term "pharmaceutically acceptable" is used to refer to a pharmaceutical excipient, it is implied that the excipient has met the required standards of toxicological and manufacturing testing and/or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration. As explained in further detail infra, "pharmacologically active" (or simply "active") as in a "pharmacologically active" derivative or analog refers to derivative or analog having the same type of pharmacological activity as the parent agent.
[00324] As used herein, the term“antigen” is defined as any substance capable of eliciting an immune response.
[00325] As used herein, the term“immunogen” refers to an antigen or a substance capable of inducing production of an antigen, such as a DNA vaccine.
[00326] The present disclosure provides libraries and arrays of glycans that can be used for identifying which types of proteins, receptors, antibodies, lipids, nucleic acids, carbohydrates and other molecules and substances can bind to a given glycan structure.
[00327] The arrays and methods of the present disclosure also provide highly accurate results. The libraries and arrays of the present disclosure provide large numbers and varieties of glycans. As a non-limiting example, the libraries and arrays of the present disclosure have at least one, at least two, at least three, at least ten, or at least 100 glycans. In some embodiments, the libraries and arrays of the present disclosure have about 1 to about 100,000, or about 1 to about 10,000, or about 1 to about 1,000, or about 1 to about 100, or about 2 to about 100, or about 2 to about 10, or about 1 to about 10 different glycans per array. Such large numbers of glycans permit the simultaneous assay of a multitude of glycan types. As described herein, the present arrays have been used for successfully screening a variety of glycan binding proteins. The composition of glycans on the arrays of the present disclosure can be varied as appropriate. Many different glyconjugates can be incorporated into the arrays of the present disclosure including, for example, naturally occurring or synthetic glycans, glycoproteins, glycopeptides, glycolipids, bacterial and plant cell wall glycans and the like.
[00328] Exemplary arrays configured suitably in accordance with various embodiments of the present disclosure include, for example, U.S. Patent No. US8383554 B2,“Quantitative Microarray of Intact Glycolipid CD1d Interaction and Correlation with Cell-Based Cytokine Production,” U.S. Patent No. US 8906832 B2 “QUANTITATIVE ANALYSIS OF CARBOHYDRATE-PROTEIN INTERACTIONS USING GLYCAN MICROARRAYS: DETERMINATION OF SURFACE AND SOLUTION DISSOCIATION CONSTANTS,” U.S. Patent No. US8680020 B2“Glycan arrays on PTFE-like aluminum coated glass slides and related methods,” U.S. Patent No. US8507660 B2“Alpha-Selective Sialyl Phosphate Donors For Preparation Of Sialosides And Sialoside Arrays For Influenza Virus Detection,” U.S. Publication No. US20150160217 (also published as WO2011130332 A1)“Glycan Arrays For High Throughput Screening Of Viruses,” all of which are herein incorporated by reference in their entirety.
[00329] The substrate may be, in some embodiments, a surface, solid surface, non- transparent solid, a solid transparent to selected wavelengths of visible or non-visible light, a particle, an array, a microbubble, or a bead. In some embodiments, the bead can be on a surface, embedded in a surface, or connected to a surface. In some embodiments the substrate may be coated.
[00330] The substrate of the present disclosure can be a surface. The surface can be flat, featured, round, curved, rough, porous, solid, gelatinous, polymeric, oligomeric, or a bead. The substrate can be composed of glass, polymer, or plastic. The bead can be round, cylindrical, egg-shaped, oval, approximately round, disc-shaped, square-shaped, hexagonal- shaped, or any polyhedral-shaped entity. In some embodiments, the substrate can be chemically modified so as to present a reactive group at the surface capable of binding to another molecule. In some embodiments, the reactive group can be a carboxylic acid. In some embodiments, the bead can be a silica bead. In some embodiments, the bead can be a silica-functionalized coated silica bead. In some embodiments, the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized silane molecule. In some embodiments, the functionalized silane molecule can be a functionalized trichlorosilane, functionalized dichlorisilane, or functionalized monochlorosilane molecule. In some embodiments, the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized tri-alkoxy functionalized silane. In some embodiments, the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized di-alkoxy functionalized silane. In some embodiments, the silica-functionalization can be a functionalization achieved by contacting the silica bead with a functionalized mono-alkoxy functionalized silane. The functionalization can be an amino, aldehyde, halide, epoxy, NHS (N-hydroxy succinimide), maleimide, alkynyl, ethynyl, carbonyl (including carboxyl) or hydroxyl functional group. In some embodiments, the functionalization can be contacted with the silane via an C1-C6 alkyl group, alkoxy group, or aryl group.
[00331] In certain aspects, immobilization procedures for attaching different glycans to the arrays of the present disclosure are readily controlled to easily permit array construction. In some embodiments, each glycan can be adhered to a specific bead type, so as to form a glycan-specific association with that bead type. In some embodiments, the bead can further comprise a distinct marker which distinguishes that particular bead type from other bead types. In some embodiments, a plurality of different glycans, each adhered to a distinct bead type can be mixed in a multiplex reaction. The bead types and multiplex reaction detection methods can be those described in U.S. Patent No. 6,696,304 and PCT Patent App. No. PCT/US2004/038416, both of which are herein incorporated by reference.
[00332] In some embodiments, the substrate can be coated with a material which can present a reactive group at the surface capable of binding to another molecule. In some embodiments, the material coating the substrate is a nitrocellulose membrane or a polymer. Such coatings present a 3D surface with high surface area, enabling a lower limit of detection compared to flat surfaces. In some embodiments an avidin, streptavidin, or neutravidin protein can be presented to the coated surface, such as a nitrocellulose membrane coating, for the attachment of biotinylated molecules. In some embodiments, a chemical linker can be presented to the surface, either directly to the surface or to a coating previously presented to the surface.
[00333] In one embodiment, the present disclosure provides linkers that may be used in a variety of applications. For example, the linkers of the present disclosure may be used to attach molecules to substrates, such as surfaces, solid surfaces, particles, arrays or beads.
[00334] In one embodiment, the present disclosure relates to a bead for use in disease diagnosis and drug discovery, the bead comprising: (a) a unique identifier on or within each bead; and (b) a glycan attached to the surface of the bead through a linker moiety. The glycan can be any of the diverse glycans described herein. In some aspects, the bead can be coated with a homogeneous population of glycan type.
[00335] In some embodiments, the present disclosure relates to methods of making glycan- linker-beads, comprising (a) providing a bead comprising a unique identifier on or within each bead; (b) contacting a glycan-linker with the bead; and (c) forming a conjugate between the glycan-linker and the bead. In some embodiments, the unique indentifier on or within each bead can be a holographic image impregnated within the silica or glass bead, a specific amino acid sequence or oligonucleotide sequence attached to each bead, or a specific fluorophore attached to each bead. In some embodiments, the specific amino acid sequence or oligonucleotide sequence attached to each bead can be further linked to a linker moiety which is further conjugated to the specific glycan attached to each bead.
[00336] In some embodiments, the present disclosure relates to glycan-linker beads made by a process comprising: (a) providing a bead comprising a unique identifier on or within each bead; (b) contacting a glycan-linker with the bead; and (c) forming a conjugate between the glycan-linker and the bead.
[00337] Immobilization procedures for attaching different glycans to the arrays of the present disclosure are readily controlled to easily permit array construction. In some embodiments, each glycan can be adhered to a specific bead type, so as to form a glycan-specific association with that bead type. In some embodiments, the bead can further comprise a distinct marker which distinguishes that particular bead type from other bead types. In some embodiments, the distinct marker can be an amino acid sequence, oligonucleotide sequence, fluorophore, or dye contacted to or within each bead type. In some embodiments, the fluorophore or dye can be those known within the art. In some embodiments, the amino acid sequence or oligonucleotide sequence can be detectected by an antibody or another oligonucleotide sequence complementary to the oligonucleotide sequence contacted to the bead. In some embodiments, the oligonucleotide sequence complimentary to the oligonucleotide sequence contacted to the bead surface can be labeled with one or a plurality of fluorophores. The fluorophores can be any of those known in the art (e.g., FAM, Cy3, Cy5, Cy 7, Cy3.5, Cy5.5, BHQ quenchers, TAMRA, ROX, Texas Red, Alexa fluors, those described in the Molecular Probes/Invitrogen/ThermoFisher catalog as of the filing date of the present application, etc.). In some embodiments, a plurality of different glycans, each adhered to a distinct bead type can be mixed in a multiplex reaction.
[00338] Arrays comprising unique libraries of different glycans adhered to defined regions on the solid support of an array surface can be adhered by any available procedure. In general, arrays are made by obtaining a library of glycan-linked glycopeptide molecules described herein, obtaining a substrate that has a surface modified to react with the specific linking moieties present on the glycan-linked glycopeptide molecules of the library and attaching the glycan molecules to the solid support by forming a van der Waals interaction between the linking moieties of the glycan-linked glycopeptide molecules and the modified surface of the substrate.
[00339] The modification reagent can be attached to the substrate via carbon-carbon bonds using, as a non-limiting example, siloxane bonds (using, for example, glass or silicon oxide, or activated silicon dioxide wherein the activated silicon dioxide is the result of the reaction of a silane molecule (e.g., those available from the Geleste, Inc. catalog as of the filing date of the present application, herein incorporated by reference), as the solid substrate). In some embodiments, siloxane bonds with the surface of the substrate are formed in via reactions of derivatization reagents bearing mono-, di-, or tri-chlorosilyl, or mono-, di-, or tri-alkoxysilyl groups. The non-leaving (chloro- or alkoxy-) groups on the silane can be hydrocarbons. In some embodiments, the non-leaving groups can be linear or branched alkyl chains so as to form van der Waals interactions with the peptide chains of the glycan-linked glycopeptide.
[00340] The modification reagent can be applied to the substrate via other deposition methods known to those skilled in the art for applying coatings. Such methods include chemical vapor deposition, solution-phase deposition, Langmuir-Blodgett film formation, chemical plasma treatment to expose a reactive surface molecule, spin-coating, spray-drying, or electrospinning. In some embodiments, the modification reagent can be a polymer. The polymer can be selected from polystyrene, polypropylene, polyethylene, polyethylimine, polycaprolactine, modified polycaprolactone, polymethyl methacrylate, polyacrylamide, poly-N,N-alkyl acrylamide, polyalkyl methacrylate, polyalkyl acrylate, a polysaccharide, or copolymers thereof. The polysaccharide can be cellulose, nitrocellulose, chitosan, amylose, cellulose acetate, xanthan gum, dextran, welan gum, guar gum, gellan gum, diutan gum or pullulan. The polysaccharide can further be functionalized by the reaction of an oxidizing group. In some embodiments, the oxidizing group can be sodium periodate. In some embodiments, the glycan can be reacted to the polysaccharide in the presence of a reducing agent. In some embodiments, the reducing agent can be a functionalized borohydride moiety. In some embodiments, the functionalized borohydride moiety can be a hydro-borohydride (e.g., sodium or potassium borohyride)), cyanoborohydride, or alkylborohydide moiety).
[00341] In some embodiments, each type of glycan can be contacted or printed onto a solid support at a defined glycan probe location. A microarray gene printer can be used for applying the various glycan-linked glycopeptide to defined glycan probe locations. For example, about 0.1 microliterto about 10 nanoliter (nL), or about 0.5 nL of glycan solution can be applied per defined glycan probe location or bead. Various concentrations of the glycan-linked glycopeptide solutions can be contacted or printed onto the solid support. For example, a glycan-linked glycopeptide solution of about 0.1 to about 1000 micromolar (μM) glycan-linked glycopeptide or about 1.0 to about 500 μM glycan-linked glycopeptide or about 10 to about 100 μM glycan-linked glycopeptide can be employed. In general, it may be advisable to apply each concentration to a replicate of several (for example, three to six) defined glycan probe locations. Such replicates provide internal controls that confirm whether or not a binding reaction between a glycan-linked glycopeptide and a test molecule is a real binding interaction.
[00342] Arrays of detector molecules are useful for detecting the presence of multiple analytes in a sample in parallel. The elements of an array of detector molecules comprises a substrate, the presentation of a coating of a bio-active molecule on the substrate, the presentation of one or a plurality of analytes to the coated substrate, the formation of a complex between the analyte and the bio-active molecule on the substrate, and a mechanism of detection. As used herein the term“bio-active molecule” means its ordinary meaning in the art and any molecule which exists or mimics a molecule known in biology or chemistry and which is capable of binding to another molecule via electrostatic, van der Waals interactions, hydrophobic interactions, covalent bonds, and/or hydrogen bonds.
[00343] The substrate of the current present disclosure can be a surface. The surface can be flat, featured, round, curved, rough, porous, solid, gelatinous, polymeric, oligomeric, or a bead. The substrate can be composed of glass, polymer, or plastic. The bead can be round, cylindrical, egg-shaped, oval, approximately round, disc-shaped, square-shaped, hexagonal- shaped, or any polyhedral-shaped entity. In some embodiments, the substrate can be chemically modified so as to present a reactive group at the surface capable of binding to another molecule. In some embodiments, the reactive group can be a carboxylic acid. [00344] In some embodiments, the substrate can be coated with a material which can present a reactive group at the surface capable of binding to another molecule. In some embodiments, the material coating the substrate is a nitrocellulose membrane or a polymer. Such coatings present a 3D surface with high surface area, enabling a lower limit of detection compared to flat surfaces. In some embodiments, a chemical linker can be presented to the surface, either directly to the surface or to a coating previously presented to the surface.
[00345] In some embodiments, the substrate can be a functionalized bead as commercialized by Illumina, Inc. with the BeadXpress, or Luminex systems, as of the filing date of the present disclosure.
General Aspects of the Present disclosure
Modular synthesis of high mannose, hybrid- and complex-type N-glycans
[00346] The exemplary method embodiment as disclosed herein is designed on the basis that diversity can be created by assembly of the so called "D1 and D2/D3 arm modules", followed by the α-specific mannosylation at the 3-O and/or 6-O position of the mannose residue of the common core trisaccharide.
Figure imgf000079_0001
[00347] Based on the retrosynthetic disconnection of N-glycan structures (Fig. 1c), the inventors surprisingly discovered that a modular set of building blocks 1-13 and the core trisaccharides 14-15 with crucial β-mannoside linkage (Fig.2) can be used as starting materials for the preparation of various N-glycans (G1-33, Supplementary Fig. S11). To demonstrate the effectiveness and utility of this strategy, the oligomannose-type (mono- to pentasaccharides, 1- 5), the complex-type (di- to heptasaccharides, 6-13) and the core trisaccharide (14-15) building blocks were first chemically synthesized on multigram scales, with temporary anomeric protecting groups installed prior to transformation into fluorides. For the high-mannose series (Man3/Man4/Man5/Man9 GlcNAc2) glycans, donors 1 and 2, and for the hybrid series glycans, donors 6 and 7 were stereoselectively linked to the 3-O position of 14. Then, the benzylidene ring was removed to get 4, 6-diol and finally a regioselective glycosylation was achieved at the 6-O position with donors 1-7. In the course of glycosylation reactions, various promoters were employed depending on the choice of glycosyl donors. The phthalimide protections at all glucosamine residues were modified to acetamides, and deacetylation and finally debenzylation were performed to obtain free glycans (Fig. S1: Glycans 1, 2, 4-9, 12). Utilizing the high specificity, the complex type D1 arm of the hybrid glycan was enzymatically sialylated to get α-2,3/6-Neu5Ac isoforms (Fig. S2- Glycans 10-11, 13-14).
[00348] Having established a rapid way to synthesize the complex type glycans (Glycans 15- 17, 20-23, 26-28 and 32-33, Supplementary Fig. S3), the inventorsset out to generate more diverse asymmetric glycans and focused on the α-2, 6-sialylated antigens recognized by PG9 and PG16 using building blocks 9-13 prepared on gram quantities (Supplementary Schemes S4-S8). Fluoride donors 8-13 were then used for the glycosidation of core 15 under the promotion of AgOTf/Cp2HfCl2. Surprisingly, all these complex conjugations were found to be very clean (Supplementary Scheme S14-S19), and the stereoselectivity was excellent. The glycosylation of 8 resulted in a mixture of isomers. At last, a global deprotection afforded naturally occurring positional isomers of bi-, tri and tetraantennary asymmetric N-glycans (Supplementary Figure S3 Glycans 18, 24, 25, 29-31). To study the role of core fucose, examples 3 and 19 were also prepared.
[00349] With this convergent synthesis strategy in place, a chemo-enzymatic approach to the synthesis of D1 and D2/D3 N-glycan arm donors was implemented to allow a rapid assembly of diverse N-glycans. Various glycosyl transferases were used, including β-1,4- galactosyltransferases, α-2,3/2,6 sialyltransferases, and α-1,3/1,2 fucosyltransferases, for the preparation of linear and branched modules by enzymatic extension of chemically synthesized acceptors 16-20 (Fig.3). The GlcNAc moiety of acceptor 16 was transformed into LacNAc by using β-1,4-galactosyltransferase and uridine 5’–diphosphogalactose (UDP-Gal) to form 21, which was further extended by α-2,6/2,3 sialyltransferase in the presence of cytidine-5’- monophospho-N-avetylneuraminic acid (CMP-Neu5Ac) to provide targets 23 and 24 respectively. Next, treatment of 21, 23-24 with the α-1,3-fucosyltransferase from Helicobacter pylori (Hpα1,3FT) resulted in the modification of LacNAc and α-2,3-sialyl LacNAc but not 2,6-sialyl LacNAc to afford 22 and 25. In addition, the α-1,3-fucosylated LacNAc was found to restrict the access of enzymatic α-2,3/6-sialylation to the terminal galactose. Acceptor 21 was modified with the α-1,2-fucosyltransferase from HEK293 cells in the presence of guanosine 5’- diphospho-β-L-fucose (GDP-fucose) to provide 26 (Fig. 3a). It was observed that the α-1,2 fucosylated module 26 was accepted by the α-2, 6 sialyltransferase to give 27, but the α-2,3 sialyltransferase failed to accept this substrate (Fig.3a and Supplementary Scheme S23). Next, the symmetric modules 28-33 were prepared from acceptors 17-18 (Fig.3b).
[00350] In the case of asymmetric modules, selective incorporation of sialic acid or fucose to one of the antennae is necessary. Therefore, acceptors 19-20 were designed in such a way that the GlcNAc at the mannose 2-O position was differentiated from the GlcNAc at the 4 or 6-O position by masking the 4-hydroxy group through acetylation to prevent enzymatic
galactosylation while retaining its water solubility. This strategy allowed a selective extension of one arm while keeping the other intact. As depicted in Fig.3c, a Gal residue was added by β- 1,4-GalT to the GlcNAc residue at the β-1,4 / 1,6 mannose branch, whereas the GlcNAc residue at the β-1,2 branch remained intact. By taking advantage of their specificity, α-1,3- FucT and α-2, 6-SiaT were used for the preparation of the asymmetric modules 36-43, and 45- 47 (Fig.3c and Supplementary Scheme S25) which were purified and fully characterized (Supplementary III).
[00351] To illustrate the use of modules prepared by the chemo-enzymatic method for further glycosylation, modules 21 and 22 were selected for the proof-of-concept experiment (Fig.4). Peracetylation of modules 21 and 22, followed by transformation into the glycosyl fluoride provided donors 50 and 51 respectively. Glycosylation with fluoride 50, in the presence of AgOTf/Cp2HfCl2, indeed provided the expected hexasaccharide 52 in 70% yield. Next, the benzylidene was cleaved in the presence of p-toluene sulfonic acid catalyst, and the donor 51 was stereospecifically installed at the 6-position to give decasaccharide 54 which was deprotected to afford glycan 55 (Supplementary Scheme S26 and S27).
[00352] Taken together, the inventorshave demonstrated an efficient way to prepare the complex type N-glycans of interest through a proper selection of a defined set of modules that are generated chemically as well as chemo-enzymatically. The versatility of oligosaccharyl fluoride donors, allowed a clean conjugation of highly branched modules to the core with excellent stereo- and regio-selectivity. The oligosaccharides with a preinstalled alkyl amine linker at the reducing end can be used directly for reaction with NHS (N-hydroxy succinimide, although epoxy functionalized slides would also work) slides through amide bond formation, or further modified or other array formats, or conjugated to proteins for structural and functional studies.
Glycan microarray on NHS-activated and aluminum oxide-coated glass slides
[00353] It was reported that PG9, PG16 and PGTs 128, 141-145 were able to neutralize 70-80% of circulating HIV-1 isolates with potent activity 20 , suggesting that the targeted epitopes are highly conserved among the HIV-1 variants, and could guide the design of immunogens. To gain insights into the glycan specificities of these antibodies, the inventorsused our newly developed array to profile the ligands of HIV-1 bNAbs. The synthetic N-glycan ligands were printed on NHS-activated glass slides through amide bond formation with 100 µM each of glycans 1-33 (Supplementary Fig. S11). Each sample was printed with five replicates and slide images were obtained from a fluorescence scan after incubation with DyLight649-conjugated donkey anti-Human IgG antibody. Our results revealed that PG16 binds to the α-2, 6-sialylated complex- type oligosaccharides, consistent with our previous results 50 , and the binding affinity is proportional to the number of terminal sialic acid residues (Supplementary Fig. S12). In addition, the inventorsfound that the PG16 binding was not affected by the presence of the core fucose (glycan 19 vs 16). Interestingly, the binding of PG16 to asymmetric glycans 29-33 suggest the importance of sialic acid on the D1 arm. Finally, the inventorscould not observe binding to the high-mannose-type glycan Man5GlcNAc2 (Supplementary Fig. S12).
Furthermore, PG9 and PGTs 141-145 were not detected to bind any of the glycans on the NHS array, probably due to their extremely weak binding. (Supplementary Fig. S13-15). In our binding studies, the inventorsobserved a strong fluorescent signal against glycan 5, Man4GlcAc2, which was later confirmed to be from the non-specific binding of secondary antibody (Supplementary Fig. S16).
[00354] To further understand why glycan binding to these bNAbs was not readily observed on the NHS-coated glass slides, the inventorsconducted a specificity test with the ACG array. A comparison of homogeneity between the ACG and NHS-coated glass slides showed that the ACG slide provided a more homogeneous glycan distribution on its surface (Supplementary Fig. S4-S9), and based on atomic force microscopy (AFM), the structural orientation of the glycans on the ACG slide was in a more extended conformation (Supplementary Fig. S10). Therefore, the inventorscan simply adjust the concentration of glycan to control the density and distance of glycans on the ACG surface. To prepare a representative ACG array, glycans I-XI (Fig. 5a) were linked to a phosphonic acid tail for spontaneous covalent immobilization on the ACG slide (Supplementary Scheme S21). After incubation with a secondary antibody, the inventorsdetermined the dissociation constant (K D.surf. )59 of the glycans interacting with the antibody of interest. Using the ACG slide, the signal intensity was enhanced, as shown by the use of PG16 at 1 µg/mL on the ACG slide in comparison to 25 µg/mL used on the NHS-coated glass slide (Fig. 5b and Supplementary Fig. S12). The binding affinity of PG16 to the bi-antennary complex-type N- glycan (XI) (K D = 0.320 µM) was higher than that to the hybrid-type glycan (X) (K D = 0.935 µM) (Supplementary Fig. S19 and Table S2), supporting the proposed existence of these glycans at Asn173 as suggested by the structural study of PG16 in complex with gp120 30 .
[00355] To evaluate whether the ACG array format could enhance the detection sensitivity, the inventorsperformed a ligand specificity profiling at various concentrations of PG9. Interestingly, on the ACG array, PG9 showed an apparent specificity for the hybrid-type glycan (X) (Fig. 5b) and detectable binding to Man 5 GlcNAc 2 (IV) and the α 2,6-sialylated bi-antennary complex-type oligosaccharide (XI). Previously, it was shown that PG9 required Man 5 GlcNAc 2 at primary (Asn160) and secondary (Asn156 or Asn173) binding sites together with a short peptide strand in gp120 recognition 26 , whereas the composition of glycan at Asn156 or Asn173 was defined as a complex-type glycan in later studies 30,31 . In the present study, the strong PG9 interaction with the hybrid-type structure compared to both Man 5 GlcNAc 2 and complex-type glycans indicated the presence of a hybrid-type glycan or an oligomannose and a complex-type glycan in close proximity as ligand(s). Nonetheless, to our knowledge, these results represent the first evidence of PG9 binding to carbohydrates without protein or peptide domains.
[00356] To understand the exact glycan epitopes recognized by antibodies PGTs 141- 145 20 , a panel of glycans I-XI on the ACG slide was prepared for analysis. The result revealed that PGTs 141-144 could recognize the oligomannose glycans Man 3/5/9 GlcNAc 2 , and the observed trend in binding affinity was PGT142 > PGT144 > PGT141 > PGT143 (Fig.5c and Supplementary Fig. S18); however, PGT145, the most potent of the group, failed to show detectable binding. The significant decrease in the affinity for PGTs 141- 144 towards Man 9 GlcNAc 2 was p r obab lydue to the shielding of the inner core
(Man 3/5 GlcNAc 2 ) by terminal mannose residues. Taken together, these results demonstrate the efficiency of the ACG array format in detecting low affinity interactions of recently isolated HIV-1 bNAbs.
Heteroglycan binding of PG9 and PG16
[00357] Due to the absence of a co-crystal structure of PG9 in complex with a hybrid-type glycan, it is difficult to determine the molecular details of the interaction. The structural features suggest that PG9 could accommodate the high-mannose-type D2/D3 arm and t h e complex-type D1 arm present in a hybrid-type glycan, or has binding sites that can accommodate Man5GlcNAc2 at Asn160 and complex-type glycans at Asn156 or 173 30,31 ; however, both complex- and hybrid-type glycans contain the α-2,6-NeuAc-Gal-GlcNAc arm.
[00358] To evaluate the glycan combination at Asn160 and Asn156/Asn173 of gp120 that best fits into the PG9 binding pocket, the inventorsprinted two different mixed-glycan arrays. In one array, Man 5 GlcNAc 2 (IV) was mixed with every glycan from I-XI in a 1:1 mole ratio (Fig. 5d), while in the other, the bi-antennary complex-type structure (XI) was mixed with every glycan from I-XI (Fig.5e). The binding profile of PG9 to various mixtures suggests that a mixture containing Man 5 GlcNAc 2 and a bi-antennary glycan [(IV+XI) or (XI+IV)] interacted more strongly with PG9 compared to IV or XI alone.
Furthermore, the inventorsalso observed a comparable binding to Man5 combined with X and XI, suggesting that Man 5 GlcNAc 2 at Asn160 was the primary binding site, while structures IX, X, and XI used the complex-type D1 arm for interaction with the secondary binding site. Based on the homogeneous array results of PG9 (Fig. 5b), Man 5 GlcNAc 2 IV or complex-type glycan XI alone did not seem to provide sufficient binding affinity; on the other hand, the hybrid-type glycan X showed a significant enhancement in binding. In the mixed glycans study (Fig.5c), however, a combination of IV and XI was found to achieve the strongest binding to PG9, followed by a combination of Man5 and hybrid type. I n a similar manner, the inventorsstudied the binding specificity of PG16 (Fig.5e), and it was found that the combination of Man 5 GlcNAc 2 and complex-type N-glycan
(IV+XI) (KD = 0.827 µM) or the combination of hybrid and complex glycans (X+XI) (K D = 0.988 µM) was weaker than the complex type glycan alone (K D = 0.320 µM) (Supplementary Fig. S19 and Table S2). These results indicate the importance of sialylated antennae in the PG16 binding site, including possibly the tri- and tetra-antennary complex-type N-glycans reported previously 50 .
[00359] To further understand the exact ratio of IV and XI in the mixture, the
inventorsperformed a serial dilution experiment. IV was mixed with XI in various ratios (1:1/2/3/4/5) and vice versa. A 100 μM solution of each of these mixtures was printed on the ACG surface together with linker and glycans alone as control.
Interestingly, at fixed IV, the PG9 binding was gradually decreased by increasing the
XI ratio in the mixture. By changing the IV ratio at fixed XI, PG9 achieved the
strongest binding at the ratio of 1:1 and 2: 1 of IV to XI (Fig.6a). These results
suggest that the glycan ratio of 1: 1 is the best ligands for PG9. However, PG16
responded in a different manner to each of these mixtures where the interactions were greatly enhanced by the presence of complex type glycan in the mixtures (Fig.6b).
However, the inventorswere unable to detect PG16 binding to Man5GlcNAc2. The inventorsconclude that PG9 recognizes a mixture of Man5 and complex type glycan, whereas, the complex type glycan alone is enough to elicit PG16 response.
Conclusion
[00360] In conclusion, the inventorshave successfully developed a modular synthetic strategy for the rapid production of a diverse array of high-mannose-, hybrid- and complex-type N-linked oligosaccharides in highly pure and sufficient amounts, making possible the study of various N-glycans and the development of new glycan array platforms to determine the glycan specificities of newly discovered HIV-1 bNAbs. The ACG array together with the binding measurements obtained in a high-throughput manner provide an effective means for detecting the extremely weak binding of HIV-1 bNAbs to glycans and enable the discovery and understanding of essential epitopes and hetero-ligands recognized by antibodies. These findings may aid speedy design of effective carbohydrate-based vaccines against HIV-1.
METHODS AND SUMMARY
[00361] All reactions were performed under an inert atmosphere using dry solvents in anhydrous conditions, unless otherwise noted. Full experimental details, glycan microarray analysis, and characterization data ( 1 H and 13 C nuclear magnetic resonance, high-resolution mass spectrometry, and Rf value) for all new compounds are included in the Supplementary Information I-III.
[00362] All patents, publications, scientific articles, web sites, and other documents and materials referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the present disclosure pertains, and each such referenced document and material is hereby incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such patents, publications, scientific articles, web sites, electronically available information, and other referenced materials or documents.
[00363] The specific methods and compositions described herein are representative of preferred embodiments and are exemplary and not intended as limitations on the scope of the present disclosure. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification, and are encompassed within the spirit of the present disclosure as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the present disclosure disclosed herein without departing from the scope and spirit of the present disclosure. The present disclosure illustratively described herein suitably may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. Thus, for example, in each instance herein, in embodiments or examples of the present present disclosure, any of the terms“comprising”,“consisting essentially of”, and“consisting of” may be replaced with either of the other two terms in the specification. Also, the terms“comprising”,“including”, containing”, etc. are to be read expansively and without limitation. The methods and processes illustratively described herein suitably may be practiced in differing orders of steps, and that they are not necessarily restricted to the orders of steps indicated herein or in the claims. It is also that as used herein and in the appended claims, the singular forms“a,”“an,” and“the” include plural reference unless the context clearly dictates otherwise. Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.
[00364] The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the present disclosure as claimed. Thus, it will be understood that although the present present disclosure has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this present disclosure as defined by the appended claims.
[00365] The present disclosure has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the present disclosure. This includes the generic description of the present disclosure with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.
[00366] Other embodiments are within the following claims. In addition, where features or aspects of the present disclosure are described in terms of Markush groups, those skilled in the art will recognize that the present disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group. Other embodiments are within the following claims. In addition, where features or aspects of the present disclosure are described in terms of Markush groups, those skilled in the art will recognize that the present disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group.
EXAMPLES:
[00367] The instant disclosure and examples herein documents the discovery of surprising efficacy and efficiency in synthesizing and generating N-glycans in arrays to achieve surprising efficacy in disease state (e.g. HIV-1) determination, prediction, and/or diagnosis.
[00368] The following table of content sets forth exemplars of embodiments of various attributes of the present disclosure:
Chemial Synthesis
Materials and Methods
[00369] All reagents were purchased from Sigma Aldrich, Across and used without further purification. Dry solvents were purchased from a commercial source without further distillation. Pulverized Molecular Sieves MS-4 Å (Aldrich) for glycosylation was activated by heating at 350 oC for 3 h. Reactions were monitored by analytical thin-layer
chromatography (TLC) in EM silica gel 60 F254 plates and visualized under UV (254 nm) and/or by staining with acidic ceric ammonium molybdate or p-anisadehyde. Flash chromatography was performed on silica gel (Merck) of 40-63 μm particle size. 1H NMR spectra were recorded on a Bruker AVANCE 600 (600 MHz) spectrometer at 25 ºC. All 1H Chemical shifts (in ppm) were assigned according to CDCl3 (δ = 7.24 ppm) and D2O (δ = 4.80 ppm). 13C NMR spectra were obtained with Bruker AVANCE 600 spectrometer and were calibrated with CDCl3 (δ = 77.00 ppm). Coupling constants (J) are reported in hertz (Hz). Splitting patterns are described by using the following abbreviations: s, singlet; brs, broad singlet; d, doublet; t, triplet; q, quartet; dd, doublet of doublet; m, multiplet. 1H NMR spectra are reported in the following order: chemical shift, multiplicity, coupling constant(s) and number(s) of protons. All NMR signals were assigned on the basis of 1H NMR, COSY, HSQC, HMQC, TOCSY, and 13C experiments. High resolution ESI mass spectra were recorded on a Bruker Daltonics spectrometer. NHS coated glass slides were purchased from SCHOTT (Nexterion H). Broadly neutralizing HIV antibodies PG9, PG16 and PGT141-145 were kindly gifted by Prof. Peter Kwong, NIH (PG9/PG16 also purchased from Polymun, Vienna Austria). PGT128 was kindly gifted by Prof. Dennis Burton, TSRI. Secondary antibody DyLight649-conjugated donkey anti-Human IgG was purchased from Jackson Immuno Research. Cytidine 5'-triphosphate (CTP), N-Acetylneuraminic acid (Neu5Ac), UDP galactose, L-fucose and Phospho (enol) pyruvic acid (PEP) were purchase from Sigma- Aldrich.
[00370] NMR Nomenclature. The individual sugar residues of highmannose, hybrid and complex type oligosaccharides have been labeled as shown below.
Figure imgf000091_0001
General Procedures S
[00371] Enzyme expression, purification and reactions:
The functional domain of α-2,3 sialyltransferase (JTFAJ-16)1 and α-2,6 sialyltransferase (JT- ISH-224)2 were obtained according to our previous report3. Enzymes β-1,4 Galactosyl Transferases from bovine milk was purchased from Sigma. Enzyme α-1, 2 Fucosyl Transferases (Human Fut2 derived from HEK-293 cells) was purchased from R&D
SYSTEMS. The enzymes used in this work including Bacteroides fragilis L- fucokinase/GDP-fucose pyrophosphorylase (FKP), pyruvate kinase (PK), pyrophosphatase (PPA), cytidine monophosphate kinase (CMK), CMP-sialic acid synthetases (CSS) and α 1– 3-fucosyltransferase from Helicobacter pylori (Hp1–3FTΔ26695) are examples of suitable recombinant enzymes that are expressed and purified in our laboratory. Enzymatic reactions with cofactor regeneration were carried out according to the procedure reported previously from our group4.
Global deprotection:
[00372] Method 1 (for glycans with -Nphthallamide protection at all glucosamine residues): A mixture of protected glycans (50 mmol) and 10 mL of ethylene diamine: nBuOH (1:4) was stirred at 90 oC for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac2O/pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by flash column chromatography (acetone: toluene, 2/8, v/v). Product was de-acetylated using sodium methoxide in MeOH (10 mL) for overnight. The reaction mixture was neutralized by using IR-120, filtered and concentrated in vacuo. The residue was purified by flash column chromatography (acetone: toluene, 3/7, v/v). Product was dissolved in 10 mL MeOH: H2O: HCOOH (6:3:1), Pd(OH)2 (50% by weight) was added and the reaction mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent, and the product was lyophilized to get desired oligosaccharides as a white color powder.
[00373] Method 2 (for glycans with -NHTroc protection at all glucosamine residues): A mixture of protected glycans (50 mmol) and lithium hydroxide (250 mmol) in 10 mL of 1, 4 dioxane: H2O (4:1) was stirred at 90 oC for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac2O: pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by C18 gel column chromatography (MeOH: H2O as an eluent). The product was de-acetylated using sodium methoxide in MeOH (10 mL) for overnight. The reaction mixture was neutralized by using IR-120, filtered and concentrated in vacuo. The residue was purified by C18 gel column chromatography (MeOH: H2O as an eluent). The product was dissolved in 10 mL MeOH: H2O: HCOOH (6:3:1), Pd(OH)2 (50% by weight) was added and the mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent. The product was lyophilized to get desired oligosaccharides as a white color powder. Enzymatic sialylation with cofactor regeneration:Glycans (5 µmol), Neu5Ac (10 µmol), ATP (0.05 µmol), CTP (1 µmol), phosphoenolpyruvate (10 µmol, monopotassium salt), cytidine monophosphate kinase (CMK, 80 units), CMP-sialic acid synthetases (CSS, 120 units), pyruvate kinase (PK, 40 units), pyrophosphatase (PPA, 40 units) and α 2,6/2,3 sialyltransferase (150 units) were dissolved in 50 µmol Tris buffer (25 mM, pH 7.5). The reaction was incubated at 37 oC with gentle agitation. Complete consumption of starting material was confirmed by mass spectrometric analysis. The reaction mixture was centrifuged and the supernatant subjected to gel filtration over P2-Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the respective products as amorphous white solids.
Enzymatic β-1, 4-galactosylation:
[00375] Glycans (1 eq.) and UDP galactose (2 eq. per galactose) were dissolved in Tris buffer (25 mM, pH 7.5) containing MnCl2 (10 mM). Enzyme β-1, 4-GalT-1 (150 units) was added to achieve a final concentration of glycan ranging from 2-5 mM. The resulting reaction mixture was incubated at 37 oC for 24 h. In di-galactosylation case, when TLC showed mono-galactosylated intermediate, additional UDP-galactose (2eq), β-1,4-GalT (100 units) were added and incubated at 37 oC until complete consumption of intermediate. The reaction mixture was centrifuged and the supernatant was subjected to gel filtration over P2- Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the respective products as amorphous white solids.
Enzymatic α–1, 2/3-fucosylation :To a solution of glycans (5 µmol), L-fucose (5 µmol), ATP (0.5 µmol), of GTP (0.5 µmol), PEP (10 µmol), and 10 mM MnCl2 in a 25 mM Tris buffer (pH 7.4) was added L-fucokinase/GDP-fucose pyrophosphorylase (FKP, 200 units), PK (200 units), PPA (200 units), and α-1,2/1,3-fucosyltransferase (200 units), and the mixture was incubated at 37 oC for overnight. The reaction mixture was centrifuged and the supernatant was subjected to gel filtration over P2-Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the respective products as amorphous white solids.
Synthesis of building blocks 1-13 S
[00377] Synthesis of mono-, tri- and pentasaccharide building blocks 1-5.
The mannosyl trichloroacetimidate building block 1 was obtained by reported procedure5. The preparation of D1 arm trisaccharide 2 of Man9GlcNAc2 began by glycosylation of mannosyl chloride S1a6 and thioglycoside acceptor S1b7 under the treatment of 2,6-di-tert- butylpyridine (DTBP) and silver triflate (AgOTf) to obtain disaccharide S1c (Scheme S1). Zemplén deacetylation of S1c at 2-O position followed by glycosylation with S1a by employing DTBP and AgOTf gave desired trisaccharide S1e in 93% yield. The leaving group modification of S1e from thioglycoside to glycosyl fluoride 2 was performed under the action of N-bromosuccinimide (NBS) and diethylaminosulfur trifluoride (DAST). The fluoride transformation provided us better results in terms of α-selectivity and excellent yield during glycosylation with chitobiose trisaccharide. Under the activation of AgOTf, the condensation of donor S1a6 and acceptor S1f7 was performed to afford trimannose 3, which was subsequently deacetylated and further di-glycosylated with S1a to afford D2/D3 arm pentasaccharide 5 in 71% yield. Compound 3 was next subjected to leaving group modification to trimannosyl fluoride 4 by using NBS and DAST in 68% yield. Careful observation of our strategy revealed that a single mannosyl chloride donor S1a and a unique DTBP/AgOTf mediated glycosylation condition was utilized to get D1, D2/D3 arm tri- and pentasaccharide intermediates in excellent yield.
Figure imgf000095_0001
[00378] Scheme S1 | Preparation of compound 1-5. i, DTBP, AgOTf, 4 Å MS, CH2Cl2, -30 oC to RT, overnight; S1c: 93%, S1e: 91%, 3: 66%, 5: 74%; ii, NaOMe, MeOH: CH2Cl2 = 1/1; S1d: 89%, S1g: 90%; iii, N-bromo succinimide (NBS), DAST, CH2Cl2, -30 oC to -10 oC; 2: 58%, 4:61%. DTBP: 2,6-di-tert-butylpyridine; DAST: Diethylaminosulfur trifluoride; AgOTf: Silver trifluromethanesulfonate.
Figure imgf000096_0001
[00379] p-Tolyl-2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O- benzyl-1-thio-α-D-mannopyranoside (S1c): To a solution of acceptor S1b (1.70 g, 3.05 mmol) and donor S1a (2.34 g, 4.58 mmol) in 20 mL CH2Cl2 was added activated 4 Å molecular sieves and stirred for 1 h at RT. In a separate flask, AgOTf (1.19 g, 4.58 mmol) and DTBP (1.03 mL, 4.58 mmol) in 10 mL of CH2Cl2 were stirred with 4 Å MS for 1 h. The flask containing the AgOTf/DTBP was cooled to -30 oC and solution containing mixture of donor and acceptor was added over 5 min. The solution was stirred with gradual warming up to room temperature over 24 h. TLC (ethyl acetate: hexane, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched with Et3N, filtered through Celite, the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4, and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in hexane) to afford S1c (2.90 g, 93%) as colorless foam TLC (ethyl acetate: hexane = 2/8 v/v): Rf = 0.35; 1H NMR (600 MHz, CDCl3): δ 7.38-7.16 (m, 30H, Ar-H), 7.11-7.09 (m, 2H, Ar-H), 7.00 (d, J = 8.4 Hz, 2H, Ar-H), 5.44 (s, 1H, H-1a), 5.51 (d, J = 2.4 Hz, 1H), 5.06 (s, 1H, H-1b), 4.88 (d, J = 11.8 Hz, 1H), 4.81 (d, J = 11.2 Hz, 1H), 4.73-4.37 (m, 10H), 4.29 (t, J = 8.9 Hz, 1H), 4.22 (s, 1H), 3.96-3.88 (m, 4H), 3.83-3.71 (m, 2H), 3.69-3.63 (m, 2H), 3.55 (d, J = 12.1 Hz, 1H), 2.26 (s, 3H, -C(O)CH3), 2.13 (s, 3H, -CH3 of STol); 13C NMR (150 MHz, CDCl3): δ 170.49, 138.75, 138.67, 138.62, 138.42, 138.32, 138.24, 137.87, 132.55, 130.51, 128.77, 128.64, 128.61, 128.56, 128.52, 128.39, 128.29, 128.20, 128.15, 128.03, 127.99, 127.94, 127.78, 127.63, 99.99, 87.78, 80.19, 78.35, 76.88, 75.48, 75.32, 75.03, 74.56, 73.46, 73.08, 72.47, 72.21, 72.18, 68.48, 69.02, 68.85, 21.42, 21.36; ESI-MS: m/z calcd for C63H66O11S; 1030.4218; found 1053.4228 (M + Na)+.
Figure imgf000097_0001
[00380] p-Tolyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-1- thio-α-D-manno pyranoside (S1d): To a solution of compound S1c (1.01 g, 0.970 mmol) in 20 mL of methanol: CH2Cl2 (1/1) was added sodium methoxide (0.024 g, 0.42 mmol), stirred at RT until TLC (ethyl acetate: hexane, 3/7) indicated formation of a product with consumption of the starting material. The reaction mixture was neutralized with IR-120, filtered and concentrated in vacuo and the residue was purified by silica gel column chromatography (0%→ 30% EA in hexane) to afford S1d (0.859 g, 89%) as a colorless oil. TLC (ethyl acetate: hexane = 3/7 v/v): Rf = 0.29; 1H NMR (600 MHz, CDCl3): δ 7.33-7.10 (m, 32H, Ar-H), 6.96 (d, J = 7.8 Hz, 1H, Ar-H), 5.56 (s, 1H, H-1), 5.11 (s, 1H, H-1), 4.85 (d, J = 10.8 Hz, 1H), 4.75 (d, J = 10.8 Hz, 1H), 4.69-4.62 (m, 3H), 4.52-4.38 (m, 6H), 4.37 (d, J = 12.1 Hz, 1H), 4.25 (d, J = 12 Hz, 2H), 4.09 (s, 1H), 3.90-3.77 (m, 4H), 3.70 (d, J = 10.8 Hz, 1H), 3.62 (dd, J = 4.8, 8.2 Hz, 1H), 3.54 (d, J = 10.2 Hz, 1H), 2.23 (s, 3H, CH3, STol); 13C NMR (150 MHz, CDCl3): δ 138.61, 138.42, 138.33, 138.24, 137.97, 137.51, 132.18, 130.38, 129.73, 128.55, 128.47, 128.38, 128.29, 128.24, 127.93, 127.91, 127.89, 127.86, 127.85, 127.78, 127.68, 127.57, 127.48, 127.45, 127.33, 101.23, 87.62, 80.06, 79.99, 76.52, 75.18, 75.01, 74.95, 94.35, 73.21, 73.18, 72.87, 72.38, 72.18, 71.69, 69.28, 68.70, 68.56, 19.45; ESI-MS: m/z calcd for C61H64O10S; 988.4112; found 1011.4125 (M + Na)+.
Figure imgf000098_0001
[00381] p-Tolyl-2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O- benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-1-thio-α-D-mannopyranoside (S1e): To a solution of acceptor S1d (2.6 g, 2.62 mmol) and donor S1a (2.01 g, 3.94 mmol) in 10 mL CH2Cl2 was added activated 4 Å molecular sieves and stirred for 1 h at RT. In a separate flask, AgOTf (1.02 g, 3.94 mmol) and DTBP (893 µL, 3.94 mmol) in 30 mL of CH2Cl2 were stirred with activated 4 Å molecular sieves for 1 h. The mixture of AgOTf /DTBP was cooled to -30 oC and a solution of donor and acceptor was added over 5 min. The solution was stirred with gradual warming up to RT over 24 h until TLC (ethyl acetate:
hexane, 2/8) indicated formation of product with consumption of starting material. The reaction was quenched with Et3N, filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4, filtered and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 20% EA in hexane) to afford S1e (3.50 g, 91%) as colorless foam. TLC (ethyl acetate: hexane = 2/8 v/v): Rf = 0.41; 1H NMR (600 MHz, CDCl3): δ 7.34- 7.11 (m, 45H, Ar-H), 7.05-7.03 (m, 2H, Ar-H), 6.93 (d, J = 7.2 Hz, 1H, Ar-H), 5.65 (s, 1H, H-1), 5.50 (d, J = 3.0 Hz, 1H, H-1), 5.10 (d, J = 3.2 Hz, 1H, H-1), 4.82 (dd, J = 3.1, 10.2 Hz, 2H), 4.75 (d, J = 12.1 Hz, 1H), 4.68 (s, 2H), 4.60-4.54 (m, 8H), 4.35-4.19 (m, 9H), 3.90-3.84 (m, 5H), 3.78-3.72 (m, 2H), 3.66-3.63 (m, 3H), 3.55-3.52 (m, 1H), 3.46 (d, J = 4.2 Hz, 1H), 3.41 (dd, J = 3.4, 9.2 Hz, 1H), 3.31 (d, J = 9.8 Hz, 1H), 2.20 (s, 3H, -C(O)CH3), 2.05 (s, 3H, CH3, STol); 13C NMR (150 MHz, CDCl3): δ 170.84, 139.12, 138.85, 138.79, 138.65, 138.60, 138.52, 138.37, 138.25, 137.94, 137.60, 132.30, 130.75, 129.97, 129.90, 128.98, 128.63, 128.52, 128.33, 128.20, 128.03, 127.88, 127.64, 100.79, 96.52, 88.06, 80.83, 80.45, 76.45, 76.42, 76.04, 75.65, 75.21.75.14, 74.69, 73.63, 73.05, 73.01, 72.95, 71.99, 71.87, 71.43, 69.66, 69.51, 69.35, 68.40, 68.34, 21.40, 21.36, 21.31; ESI-MS: m/z calcd for C90H94O16S; 1462.6155; found 1485.6190 (M + Na)+.
Figure imgf000099_0001
[00382] 2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-α-D- mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-1-α-D-mannopyranosyl fluoride (2): To a solution of trisaccharide S1e (0.600 g, 0.410 mmol) in CH2Cl2 (10 mL) at -30 oC was added NBS (0.218 mg, 1.23 mmol), stirred for 10 minutes. DAST (324 µL, 2.46 mmol) was added slowly and the resulting reaction mixture was stirred at -10 oC for 6 h. TLC (ethyl acetate: hexane, 3/7) indicated formation of product with consumption of starting material, the reaction was quenched with aq.NaHCO3, and the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4, filtered and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 25% EA in hexane) to afford fluoride 2 (0.320 g, 58%) as white foam and 0.200 g alcohol (anomeric-OH) as side product. TLC (ethyl acetate: hexane = 3/7, v/v): Rf = 0.31; 1H NMR (600 MHz, CHCl3): δ 7.32-7.12 (m, 45H, Ar-H), 5.67 (d, J = 50.4 Hz, 1H, Ar-H), 5.49 (s, 1H, H-1), 5.16 (s, 1H, H-1), 4.99 (s, 1H, H-1), 4.82-4.77 (m, 3H), 4.65-4.38 (m, 15H), 4.30 (d, J = 12.1 Hz, 1H), 4.03 (s, 1H), 3.97-3.94 (m, 3H), 3.90-3.64 (m, 11H), 3.54 (d, J = 10.2 Hz, 1H), 2.11 (s, 3H, -C(O)CH3); 13C NMR (150 MHz, CDCl3): δ 170.44, 138.77, 138.64, 138.60, 138.54, 138.46, 138.41, 138.28, 128.76, 128.64, 128.61, 128.54, 128.44, 128.31, 128.19, 128.13, 128.09, 128.04, 128.01, 127.95, 127.90, 127.87, 127.84, 127.79, 127.73, 107.65, 106.19, 101.04, 99.72, 78.56, 78.31, 75.45, 75.41, 75.31, 74.86, 74.59, 74.31, 74.10, 73.86, 73.68, 73.65, 73.57, 72.69, 72.49, 72.38, 72.17, 69.51, 69.31, 69.01, 68.95, 21.44; ESI-MS: m/z calcd for C83H87FO16; 1358.5870; found 1381.5891 (M + Na)+.
Figure imgf000100_0001
[00383] p-Tolyl-2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O-acetyl- 3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→6)-2,4-di-O-benzyl-1-thio-α-D- mannopyranoside (3): To a solution of acceptor S1f (0.545 g, 1.23 mmol) and donor S1a (1.57 g, 3.07 mmol) in CH2Cl2 (10 mL) was added 4 Å activated MS and stirred for 1 h at room temperature. In a separate flask, AgOTf (0.787 g, 3.07 mmol) and DTBP (690 µL, 3.07 mmol) in 10 mL of CH2Cl2 were stirred with MS 4 Å. After stirring for 1 h, the flask containing the AgOTf /DTBP was cooled to -30 oC and a solution containing a mixture of donor and acceptor was added over 5 min. The solution was stirred with gradual warming up to room temperature over 24 h. TLC (ethyl acetate: hexane, 2/8) indicated formation of product with consumption of starting material. The reaction was quenched with Et3N, filtered through Celite, the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4, filtered and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 20% EA in hexane) to afford 3 (1.10 g, 66%) as colorless foam. TLC (ethyl acetate: hexane = 2/8, v/v): Rf = 0.36; 1H NMR (600 MHz, CDCl3): δ 7.35-7.10 (m, 32H, Ar-H), 7.05 (d, J = 8.0 Hz, 2H, Ar-H), 5.51 (s, 1H), 5.47 (s, 1H, H-1), 5.45 (dd, J = 2.0, 2.8 Hz, 1H), 5.21 (s, 1H, H-1), 4.91 (d, J = 1.5 Hz, 1H, H-1), 4.86 (t, J = 10.2 Hz, 2H), 4.75 (d, J = 11.2 Hz, 1H), 4.67-4.58 (m, 5H), 4.54-4.36 (m, 8H), 4.23 (dd, J = 3.9, 9.6 Hz, 1H), 4.12-4.06 (m, 2H), 4.01 (dd, J = 3.2, 9.2 Hz, 1H), 3.97-3.86 (m, 5H), 3.82 (t, J = 9.2 Hz, 1H) 3.79-3.75 (m, 1H), 3.72 (dd, J = 3.9, 10.7 Hz, 1H), 3.70-3.56 (m, 4H), 2.17 (s, 3H, -C(O)CH3), 2.13 (s, 3H, -C(O)CH3), 2.09 (s, 3H, CH3, STol); 13C NMR (150 MHz, CDCl3): δ 170.27, 170.10, 138.57, 138.53, 138.18, 138.16, 137.81, 137.77, 137.42, 131.46, 130.85, 129.83, 128.44, 128.42, 128.36, 128.27, 128.21, 128.06, 127.81, 127.72, 127.68, 127.63, 127.53, 127.48, 99.83, 98.17, 85.23, 78.98, 78.08, 77.76, 75.15, 74.98, 74.89, 74.32, 74.15, 73.52, 73.30, 72.23, 72.05, 71.85, 71.48, 71.43, 71.36, 69.05, 68.72, 68.60, 68.41, 66.60, 60.39, 21.15, 21.00, 20.94; ESI-MS: m/z calcd for C85H90O17S; 1414.5791; found 1437.5821 (M + Na)+.
Figure imgf000101_0001
[00384] p-Tolyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-3,4,6-tri-O-benzyl-α-D- manno pyranosyl-(1→6)]-2,4-di-O-benzyl-1-thio-α-D-mannopyranoside (S1g): To a solution of trisaccharide 3 (1.30 g, 0.918 mmol) in 10 mL methanol: CH2Cl2 (1/1) was added sodium methoxide (0.024 g, 0.459 mmol), stirred at RT until TLC (ethyl acetate: hexane, 3/7) indicated formation of a product with consumption of the starting material. The reaction mixture was neutralized with IR-120, filtered and concentrated in vacuo and the residue was purified by silica gel column chromatography (0%→ 25% EA in hexane) to afford S1g (1.10 g, 90%) as a colorless oil. TLC (ethyl acetate : hexane = 3/7, v/v): Rf = 0.26; 1H NMR (600 MHz, CDCl3): δ 7.36-7.12 (m, 42H, Ar-H), 7.06 (d, J = 8.0 Hz, 2H, Ar-H), 5.46 (s, 1H, H-1), 5.24 (s, 1H, H-1), 5.01 (d, J = 1.1 Hz, 1H, H-1), 4.82 (t, J = 11.1 Hz, 2H), 4.69 (d, J = 11.6 Hz, 1H), 4.65-4.44 (m, 13H), 4.23 (dd, J = 4.1, 9.6 Hz, 1H), 4.16 (s, 1H), 4.07 (dd, J = 2.8, 9.4 Hz, 1H), 4.03 (d, J = 10.1 Hz, 1H), 3.96-3.88 (m, 4H), 3.87-3.81 (m, 3H), 3.80-3.75 (m, 1H), 3.73-3.64 (m, 4H), 3.62 (dd, J = 1.6, 10.8 Hz, 1H), 2.38 (s, 1H), 2.34 (s, 1H, - C(O)CH3), 2.19 (s, 3H, CH3, STol); 13C NMR (150 MHz, CDCl3): δ 138.12, 138.11, 137.69, 131.75, 130.12, 128.82, 128.76, 128.73, 128.67, 128.63, 128.57, 128.54, 128.53, 128.41, 128.35, 128.29, 128.19, 128.12, 128.08, 128.03, 127.95, 128.92, 127.82, 124.43, 99.90, 85.55, 80.32, 80.00, 78.49, 79.46, 75.46, 75.41, 75.27, 75.19, 75.13, 74.66, 74.50, 74.39, 73.85, 73.81, 73.62, 72.32, 72.24, 71.85, 71.71, 71.40, 71.33, 69.48, 69.00, 68.96, 68.90, 68.32, 66.51, 21.15; ESI-MS: m/z calcd for C81H86O15S; 1330.5580; found 1353.5614 (M + Na)+.
Figure imgf000102_0001
[00385] 2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O-acetyl-3,4,6-tri-O- benzyl-α-D-mannopyranosyl-(1→6)-2,4-di-O-benzyl-α-D-mannopyranosyl fluoride (4): To a solution of compound 3 (0.270 g, 0.197 mmol) in CH2Cl2 (10 mL) at -30 oC was added NBS (0.052 g, 0.296 mmol), stirred for 10 min. DAST (52 µL, 0.395 mmol) was then added slowly and the resulting reaction mixture was stirred for 4 h at -10 °C. TLC (ethyl acetate: hexane, 3/7) indicated formation of product with consumption of starting material. The reaction mixture was quenched with aq.NaHCO3, and the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 8% EA in toluene) to afford 4 (0.150 g, 61%) as white foam. TLC (ethyl acetate: toluene =1/9, v/v): Rf = 0.19; 1H NMR (600 MHz, CHCl3): δ 7.29-7.10 (m, 40H, Ar-H), 5.50 (s, 1H, H-1), 5.47 (d, J = 50 Hz, 1H, H-1), 5.46 (s, 1H, H-1), 5.18 (s, 1H), 4.92 (s, 1H), 4.86 (d, J = 11.2 Hz, 1H), 4.83 (d, J = 10.8 Hz, 1H), 4.72 (d, J = 10.0 Hz, 1H), 4.72-4.56 (m, 6H), 4.48-4.40 (m, 7H), 4.10 (d, J = 8.9 Hz, 1H), 4.00-3.92 (m, 4H), 4.90-3.77 (m, 5H), 3.71-3.64 (m, 5H), 3.57 (d, J = 7.2 Hz, 1H), 2.13 (s, 3H, -C(O)CH3), 2.06 (s, 3H, - C(O)CH3); 13C NMR (150 MHz, CHCl3): δ 170.56, 170.36, 138.80, 138.74, 138.50, 138.39, 138.11, 138.04, 137.89, 137.88, 129.70, 128.81, 128.70, 128.68, 128.65, 128.58, 128.56, 128.54, 128.43, 128.27, 128.18, 128.12, 128.07, 128.04, 128.00, 127.97, 127.89, 127.82, 126.55, 106.66, 105.18, 100.02, 98.84, 98.81, 78.31, 77.70, 76.31, 76.03, 75.42, 75.37, 75.23, 74.62, 74.41, 74.27, 73.90, 73.80, 73.65, 73.16, 72.66, 72.14, 71.92, 71.58, 69.42, 68.96, 68.70, 68.61, 66.53, 42.20, 32.21, 29.98, 29.65, 22.98, 21.63, 21.44, 21.27, 14.71, 14.41; ESI-MS: m/z calcd for C78H83O17 F; 1310.5507; found 1333.5536 (M + Na)+.
Figure imgf000103_0001
[00386] p-Tolyl-2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O- benzyl-α-D-mannopyranosyl-(1→3)-[2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl- (1→2)-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→6)]-2,4-di-O-benzyl-1-thio-α-D- mannopyranoside (5): To a solution of acceptor S1g (1.01 g, 0.739 mmol) and donor S1a (0.947 g, 1.84 mmol) in 20 mL CH2Cl2 was added 4 Å activated MS and stirred for 1 h at room temperature. In a separate flask, AgOTf (0.472 g, 1.85 mmol) and DTBP (415 µL, 1.85 mmol) in 10 mL of CH2Cl2 were stirred with MS 4 Å. After stirring for 1 h, the flask containing the AgOTf /DTBP was cooled to -30 °C and a solution containing a mixture of donor and acceptor in CH2Cl2 was added over 5 min. The solution was stirred with gradual warming up to room temperature over 24 h. TLC (ethyl acetate: hexane, 3/7) indicated formation of product with consumption of starting material. The reaction was then quenched with Et3N, filtered through Celite, and the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4, filtered and concentrated in vacuo. The residue was purified by silica gel column chromatography (0% → 25% EA in hexane) to afford 5 (1.25 g, 74%) as white solid. TLC (ethyl acetate: hexane =3/7, v/v): Rf = 0.33; 1H NMR (600 MHz, CDCl3): δ 7.27-7.04 (m, 72H, Ar-H), 7.02 (d, J = 8.0 Hz, 2H, Ar-H), 5.52 (d, J = 1.5 Hz, 2H, 2 x H-1), 5.46 (s, 1H, H-1), 5.18 (s, 1H, H-1), 5.04 (d, J = 8.2 Hz, 1H), 4.85 (t, J = 11.0 Hz, 2H), 4.78 (t, J = 11.1 Hz, 2H), 4.72-4.44 (m, 18H), 4.41-4.30 (m, 8H), 4.27 (d, J = 12.3 Hz, 2H), 4.20 (s, 2H), 4.05-3.92 (m, 6H), 3.91- 3.73 (m, 8H), 3.68-3.56 (m, 6H), 3.48 (d, J = 10.1 Hz, 1H), 3.40 (d, J = 10.3 Hz, 1H), 3.34 (d, J = 10.5 Hz, 1H), 2.10 (s, 6H, -C(O)CH3), 2.01 (s, 3H, CH3, STol); 13C NMR (150 MHz, CDCl3): δ 170.22, 152.99, 152.78, 152.57, 138.43, 138.38, 138.24, 138.05, 138.02, 137.86, 137.81, 131.15, 129.80, 128.44, 128.30, 128.20, 128.05, 127.95, 127.85, 127.72, 127.70, 127.62, 127.55, 127.53, 127.47, 127.41, 127.38, 127.35, 127.23, 126.94, 101.16, 99.37, 98.86, 84.97, 79.24, 78.07, 78.02, 75.22, 74.99, 74.87, 74.77, 74.55, 74.47, 74.29, 74.17, 73.94, 73.82, 73.38, 73.24, 73.18, 73.01, 72.58, 71.93, 71.85, 71.77, 71.60, 71.55, 71.47, 70.99, 69.41, 68.64, 68.57, 68.46, 68.01, 29.69, 21.22, 20.91; ESI-MS: m/z calcd for C139H146O27S; 2279.9698; found 2302.9747 (M + Na)+.
[00387] Synthesis of disaccharides building block 6.
[00388] Condensation of acceptor S2a8 with donor S2b9 mediated by NIS and TfOH supplied the disaccharide S2c with exclusively β-linkage (J1’,2’ = 8.5 Hz) in 64% yield. Compound S2c was next modified to fluoride 6 via anomeric deallylation followed by conversion of free -OH to -F in presence of DAST (Scheme S2).
Figure imgf000105_0001
[00389] Scheme S2 | Preparation of compound 6. i, NIS, TfOH, CH2Cl2, 4 Å MS, -40 °C, 2h, 64%; ii, (1) PdCl2, MeOH: CH2Cl2 = 1/1, (2) DAST, CH2Cl2, -30 °C to -10 °C, 3-5 h, 61%.
Figure imgf000105_0002
[00390] Allyl-O-4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl- (1→2)-O-3,4,6-tri-O-benzyl-α-D-mannopyranoside (S2c): A mixture of thioglycoside donor S2b (2.33 g, 3.65 mmol), acceptor S2a(1.50 g, 3.05 mmol) and activated 4 Å molecular sieves (3 g) in 30 mL dry CH2Cl2 was stirred for 1h at room temperature. NIS (1.35 g, 6.01 mmol) and TfOH (66.2 µL, 0.75 mmol) were added slowly at -40 oC and stirred for 2 h until TLC (ethyl acetate: toluene, 1/9) indicated formation of product with consumption of starting material. The reaction mixture was quenched with Et3N, filtered through Celite, and the filtrate was washed with aq. NaHCO3 (2 x 50 mL), aq.Na2S2O3 (2 x 50 mL) and finally with brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S2c (2.10 g, 64%) as white solid. TLC (ethyl acetate: toluene = 1/9, v/v): Rf = 0.29; 1H NMR (600 MHz, CDCl3): δ 7.52-7.50 (m, 4H, Ar-H), 7.33-7.10 (m, 16H, Ar- H), 7.10-7.09 (m, 4H, Ar-H), 7.00-6.90 (m, 2H, Ar-H), 6.89-6.81 (m, 3H, Ar-H), 5.73-5.71 (m, 1H, -OCH2-CH=CH2), 5.26 (d, J = 8.4 Hz, 1H,H-1), 5.14-5.06 (m, 3H), 4.71 (t, J = 7.8 Hz, 2H), 4.58 (d, J = 12.1 Hz, 1H), 4.50-4.39 (m, 6H), 4.34 (d, J = 4.8 Hz, 1H), 4.32 (d, J = 6.6 Hz, 1H), 4.10 (t, J = 8.6 Hz, 1H), 4.07-4.00 (q, 2H), 3.78 (dd, J = 3.2, 6.1 Hz, 1H), 3.81- 3.78 (m, 2H), 3.71-3.70 (dd, J =3.2, 6.3 Hz, 1H), 3.65-3.60 (m, 1H), 3.58 (dd, J = 3.1, 6.5 Hz, 1H), 3.56 (t, J = 8.9 Hz, 1H), 3.48 (t, J = 10.2 Hz, 1H), 3.39 (d, J = 8.4 Hz, 1H), 2.97-2.96 (m, 1H), 1.93 (s, 3H, -C(O)CH3); 13C NMR (150 MHz, CDCl3): δ 169.9, 138.69, 138.6, 138.5, 137.9, 137.9, 134., 133.8, 133.7, 131.9, 130.3, 128.5, 128.4, 128.4, 128.3, 128.2, 128.0, 127.9, 127.7, 127.7, 127.6, 127.5, 127.5, 123.3, 117.5, 97.1, 96.4, 77.9, 76.9, 75.1, 74.8, 73.9, 73.8, 73.8, 73.05, 72.8, 71.9, 71.0, 70.4, 70.1, 68.1, 55.5, 28.7, 21.5, 21.1; ESI-MS: m/z calcd for C60H61NO13; 1003.4035 found 1026.4043 (M + Na)+.
Figure imgf000106_0001
[00391] 4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)-O- 3,4,6-tri-O-benzyl-α-D-mannopyranosyl fluoride (6): To a solution of S2c (0.750 g, 0.747 mmol) in 10 mL CH2Cl2: MeOH (1/1) was added PdCl2 (0.02 g) and stirred at rt for overnight until TLC (ethyl acetate: toluene, 2/8) indicated formation of a product with consumption of the starting material. The reaction mixture was then concentrated in vacuo, and the residue was purified by flash column chromatography to afford alcohol (0.6 g, 80%) as colorless foam. To a solution of alcohol (0.270 g, 0.197 mmol) in CH2Cl2 (10 mL) at -30 oC was DAST (52 µL, 0.395 mmol) and the resulting reaction mixture was stirred at -10 °C for 8 h until TLC indicated formation of product with consumption of starting material. The reaction was quenched with aq.NaHCO3, and the filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0% → 25% EA in hexane) to afford 6 (0.150 g, 61%) as white foam. TLC (ethyl acetate: hexane =3/7, v/v): Rf = 0.45; 1H NMR (600 MHz, CDCl3): δ 7.57-7.55 (m, 4H, Ar-H), 7.35-7.21 (m, 11H, Ar-H), 7.07 (d, J = 6.4 Hz, 4H, Ar-H), 6.99 (d, J = 7.2 Hz, 2H, Ar-H), 6.88-6.82 (m, 3H, Ar-H), 5.30 (d, J = 50.4 Hz, 1H, H-1Man), 5.30 (d, J = 12.2 Hz, 1H, H-1GlcNAc), 4.88 (d, J = 11.2 Hz, 1H), 4.80-4.71 (m, 3H), 4.64 (d, J = 11.3 Hz, 1H), 4.49-4.46 (m, 2H), 4.43 (d, J = 11.8 Hz, 2H), 4.34-4.28 (m, 3H), 4.23 (dd, J = 6.1, 11.3 Hz, 1H), 4.16 (s, 1H), 4.06 (d, J = 12.1 Hz, 1H), 4.02 (d, J = 12.3 Hz, 1H), 3.76-3.57 (m, 5H), 3.32 (d, J = 10.8 Hz, 1H), 3.02 (dd, J = 4.2, 11.3 Hz, 1H), 1.97 (s, 3H, -C(O)CH3); 13C NMR (150 MHz, CDCl3): δ 170.99, 138.40, 138.28, 138.16, 137.94, 137.70, 133.94, 131.82, 128.90, 128.63, 128.57, 128.47, 128.40, 128.31, 128.27, 128.04, 127.89, 127.89, 127.76, 123.54, 106.33, 104.85, 97.45, 79.55, 78.48, 75.43, 75.23, 74.09, 73.84, 73.70, 73.16, 72.78, 72.54, 71.36, 69.18, 63.40, 55.80, 31.21, 29.98, 21.11; ESI-MS: m/z calcd for C57H56FNO12; 965.3679 found
988.3690 (M + Na)+.
[00392] Synthesis of trisaccharide building blocks 7 and 8.
[00393] Building block 7 (Figure 2a) was obtained according to previous report3. The N- pthallamide protection at Glucosamine residues was modified to NH-Troc to prepare building block 8 (Scheme S3).
Figure imgf000107_0001
[00394] Scheme S3 | Preparation of compound 8. i, (1) EDA, n-BuOH, 90 oC, (2) Troc-Cl, NaHCO3, CH2Cl2, ii, Ac2O, pyridine, RT, overnight, 72% over 3 steps; iii, (1) PdCl2, MeOH: CH2Cl2, (2) DAST, CH2Cl2, -30 oC, 66% over 2 steps.
Figure imgf000108_0001
[00395] Allyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di- benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→2)-O- 3,4,6-tri-O-benzyl-α-D-mannopyranoside (S3b): A mixture of compound S3a (1 g, 0.693 mmole) and 10 mL of ethylene diamine: n-BuOH (1:4) was stirred at 90 oC overnight.
Volatiles were evaporated, and the crude product was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (0.376 g, 6.93 mmol) and 2,2,2-trichloro ethyl chloroformate (0.665 mL, 6.93 mmol) were added at 0 oC, allowed it to warm to rt and stirred for overnight. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material. The reaction mixture was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in toluene). The product was then acetylated using 10 mL of pyridine/acetic anhydride (6:4) until TLC indicated (ethyl acetate: toluene, 2/8) complete consumption of starting material. The reaction mixture was then concentrated in vacuo and purified by silica gel column chromatography to afford S3b (0.760 g, 72%) as a white foam. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; 1H NMR (600 MHz, CDCl3): δ 7.34-7.13 (m, 40H, -Ph), 5.86-5.77 (m, 1H, allyl -CH), 5.30-5.28 (t, J = 8.2 Hz, 1H, H2gal), 5.25 (bd, 1H, -NHTroc), 5.16 (d, J = 17.6 Hz, 1H, Troc), 5.10 (d, J = 10.2 Hz, 1H), 4.90 (t, 3H), 4.82- 4.76 (m, 3H), 4.74 (s, 1H), 4.65-4.61 (dd, J = 8.4 & 2.8 Hz, 3H), 4.55-4.41 (m, 8H), 4.30 (d, J = 12.3 Hz, 2H), 4.20 (d, J = 12.2 Hz, 2H), 4.10-4.01 (m, 3H), 3.90-3.84 (m, 5H), 3.76-3.61 (m, 5H), 3.55-3.40 (m, 3H), 3.35-3.30 (m, 3H), 3.13 (d, J = 7.2 Hz, 1H), 1.92 (s, 3H, - C(O)CH3) ; 13C NMR (150 MHz, CDCl3): δ 170.23, 154.11, 139.17, 138.98, 138.75, 138.25, 138.20, 134.04, 127.41, 100.7, 97.5, 96.80, 80.55, 78.53, 75.36, 72.87, 73.55, 72.78, 72.49, 72.10, 71.96, 69.98, 68.90, 68.65, 57.64, 41.51, 21.30. ESI-MS: m/z calcd for C82H88Cl3N1O18; 1458.4960 found 1504.4956 (M + Na)+.
Figure imgf000109_0001
[00396] 2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→2)-O-3,4,6-tri-O- benzyl-α-D-mannopyranosyl fluoride (8): PdCl2 (0.030 g) was added to a solution of S3b (1.3 g, 0.942 mmol) in 10 mL of CH2Cl2: MeOH (1:1). The reaction mixture was stirred at room temperature for 2 h until TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of the starting material. The reaction mixture was then filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography to afford 1-OH compound (0.980 g) as white color foam. The residue (0.850 g, 0.608 mmol) was dissolved in CH2Cl2 (10 mL) at -30 oC, then DAST (160 µL, 1.21 mmol) was added slowly. The resulting reaction mixture was stirred for 1 h. When TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in toluene) to afford 8 (0.700 g, 66% over 2 steps) as white foam. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; 1H NMR (600 MHz, CDCl3): δ 7.35-7.10 (m, 40H), 4.57 (d, J = 51.4 Hz, 1H), 5.33 (t, J = 10.2 Hz, 1H), 5.22 (d, J = 8.2 Hz, 1H), 4.99-4.91 (m, 3H), 4.82 (d, J = 7.8 Hz, 1H), 4.75 (t, J = 10.3 Hz, 1H), 4.64-4.44 (m, 12H), 4.38 (dd, J = 3.4 & 10.2 Hz, 2H), 4.26 (s, 2H), 4.06-4.33 (m, 5H), 3.76-3.64 (m, 4H), 3.54-3.46 (m, 2H), 3.40-3.34 (m, 3H), 3.12 (d, J = 8.4 Hz, 1H), 1.65 (S, 3H); 13C NMR (150 MHz, CDCl3): δ 169.5, 154.0, 139.0, 138.8, 138.7, 138.5, 138.4, 138.3, 138.1, 129.4, 128.7, 128.6, 128.4, 128.2, 128.0, 127.9, 127.7, 127.5, 127.4, 127.2, 127.1, 125.5, 107.6, 105.4, 100.7, 98.7, 95.8, 80.5, 77.4, 74.3, 73.6, 73.3, 73.1, 72.3, 72.1, 72.0, 71.9, 68.9, 68.7, 68.3, 57.4, 41.4, 21.7, 21.2; ESI-MS: m/z calcd for C79H83Cl3FN1O17; 1443.4602 found 1466.4608 (M + Na)+.
[00397] Synthesis of complex type D1 arm tetrasaccharide 9.
[00398] Preparation of sialylated D1 arm was achieved through coupling of two main building units S4c and S4d. Use of sialyl phosphate donor S4a for the α-2,6 glycosylation of Gal S4b resulted in complete α-selectivity10. The N-Phth protection at glucosamine of S2c was modified NHTroc, while doing so, the 4-OAc group was removed to afford the desired S4d. At last the coupling of S4c and S4d afforded the desired tetrasaccharide, which further underwent anomeric modification to get donor 9.
Figure imgf000110_0001
Figure imgf000111_0001
[00399] Scheme S4 | Preparation of compound 9. i, TMSOTf, CH2Cl2, -50 oC, 64%; ii, (1) EDA, n-BuOH, 90 oC, (2) Troc-Cl, NaHCO3, CH2Cl2, 78% over 2 steps; iii, NIS, TfOH, CH2Cl2, -50 oC, 65%; iv, (1) PdCl2, MeOH: CH2Cl2, (2) DAST, CH2Cl2, -30 oC, 55% over 2 steps.
Figure imgf000111_0002
[00400] Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2- ulopyranosylonate-(2→6)-p-tolyl-4-O-benzyl-2,3-di-O-benzoyl-1-thio-β-D-glacto- pyranoside (S4c): A mixture of donor S4a (0.113 g, 0.178 mmol), acceptor S4b (0.220 g, 0.119 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at rt for 1 h. The reaction was cooled to -50 oC, trimethylsilyl triflate (12 µL, 0.06 mmol) was added slowly and the resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite, extracted with saturated NaHCO3, dried over sodium sulfate and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 25% EA in hexane) to afford S4c (0.190 g, 64%) as colorless foam. TLC: (ethyl acetate: hexane = 3/7, v/v): Rf = 0.46; 1H NMR (600 MHz, CDCl3): δ 7.93 (d, J = 7.8 Hz, 2H), 7.89 (d, J = 8.4 Hz, 2H), 7.50-7.45 (m, 2H), 7.42-7.30 (m, 6H), 7.24-7.13 (m, 5H), 7.04 (d, J = 8.2 Hz, 2H), 5.80 (t, J = 10.3 Hz, 1H), 5.47 (d, J = 8.9 Hz, 1H), 5.37 (s, 3H), 5.32 (dd, J = 4.2 & 7.8 Hz, 1H), 5.12 (dd, J = 4.1 & 7.2 Hz, 1H), 4.90 (d, J = 12.2 Hz, 1H), 4.65 (d, J = 12.1 Hz, 1H), 4.20 (dd, J = 3.2 & 7.8 Hz, 1H), 4.18 (d, J = 6.8 Hz, 1H), 3.94-3.91 (m, 3H), 3.74-3.72 (m, 3H), 3.71 (s, 3H), 3.65 (dd, J = 3.2 & 7.8 Hz, 1H), 3.06 (t, J = 10.2 Hz, 2H), 2.87 (dd, J = 3.6 & 8.6 Hz, 1H), 2.33 (s, 3H), 2.17 (s, 3H), 2.15 (t, J = 7.8 Hz, 1H), 2.13 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 171.9, 170.8, 169.8, 168.2, 166.8, 165.2, 159.2, 138.1, 133.7, 133.3, 130.0, 129.8, 129.4, 129.3, 129.2, 128.7, 128.6, 128.5, 128.4, 127.8, 127.7, 125.5, 100, 5, 86.8, 76.8, 76.1, 74.7, 73.8, 68.9, 68.5, 68.3, 67.2, 63.7, 62.0, 58.1, 53.3, 37.7, 25.88, 21.7, 21.5, 21.3, 21.0, 20.9 ; ESI-MS: m/z calcd for C51H53NO18S; 999.2876 found 1022.2882 (M + Na)+.
Figure imgf000112_0001
[00401] Allyl-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- gluco-pyranosyl-(1→2)-O-3,4,6-tri-O-benzyl-α-D-mannopyranoside (S4d): A mixture of compound S2c (2 g, 1.99 mmole) and 20 mL of ethylene diamine: n-BuOH (1:4) was stirred at 90 oC overnight. Volatiles were evaporated, and the crude product was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (1.05 g, 19.9 mmol) and 2,2,2- trichloro ethyl chloroformate (1.9 mL, 19.9 mmol) were added at 0 oC, allowed it to warm to rt and stirred for overnight until TLC (ethyl acetate: toluene, 1.5/8.5) indicated formation of product with consumption of starting material. The reaction mixture was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 10% EA in toluene) to afford S4d (1.5 g, 78%) as a white foam. TLC (ethyl acetate: toluene = 1.5/8.5, v/v): Rf = 0.44; 1H NMR (600 MHz, CDCl3): δ 7.30-7.15 (m, 25H), 5.87-7.78 (m, 1H), 5.33 (d, J = 5.2 Hz, 1H), 5.21 (d, J = 3.2 Hz, 1H), 5.14 (d, J = 7.2 Hz, 1H), 4.94 (d, J = 5.8 Hz, 1H), 4.80 (d, J = 8.5 Hz, 1H), 4.73-4.44 (m, 10H), 4.12-4.06 (m, 3H), 3.97-3.86 (m, 3H), 3.78-3.49 (m, 7H); 13C NMR (150 MHz, CDCl3): δ 153.97, 138.45, 138.37, 138.28, 137.98, 137.45, 133.63, 128.94, 128.43, 128.40, 128.26, 128.16, 127.97, 127.91, 127.78, 127.65, 127.53, 127.41, 125.20, 117.23, 97.93, 96.88, 95.50, 79.33, 79.08, 75.08, 74.47, 74.37, 73.53, 73.19, 73.00, 71.98, 71.65, 70.83, 69.16, 67.91, 57.41, 44.53; ESI-MS: m/z calcd for C53H58Cl3NO12; 1005.3025 found 1006.3089 (M + H)+.
Figure imgf000113_0001
[00402] Allyl-[Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto- non-2-ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galactopyranosyl- (1→4)-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranosyl-(1→2)-O-3,4,6-tri-O-benzyl-α-D-mannopyranoside (S4e): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S4d (0.208 g, 0.169 mmol) and donor S4c (0.310 g, 0.199 mmol) in anhydrous CH2Cl2 (10 mL). The mixture was stirred for 1 h at room temperature. The reaction mixture was cooled to -50 oC, NIS (0.076 g, 0.338 mmol) and TfOH (3.7 µL, 0.042 mmol) were added slowly. The resulting reaction mixture was stirred for 2 h. When TLC (ethyl acetate: toluene, 1.5/8.5) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S4e (390 g, 65%) as clear foam. TLC (ethyl acetate: toluene = 1.5/8.5, v/v): Rf = 0.51; 1H NMR (600 MHz, CDCl3): δ 7.91-7.85 (m, 4H, Ph), 7.50-7.46 (m, 1H, Ph), 7.35-7.19 (m, 35H), 5.82-5.76 (m, 2H), 5.39-5.36 (m, 3H), 5.24 (d, J = 6.4 Hz, 1H), 5.22 (d, J = 7.2 Hz, 1H), 5.19 (d, J = 3.4 Hz, 1H), 5.15 (d, J = 3.4 Hz, 1H), 5.11-5.08 (dd, J = 6.3 & 3.1 Hz, 2H), 4.96 (d, J = 12.1 Hz, 2H), 4.83 (d, J = 12.1 Hz, 2H), 4.73-4.57 (m, 10H), 4.47-4.42 (m, 6H), 4.25-4.15 (m, 8H), 4.08-3.93 (m, 10H), 3.91 (s, 3H,), 3.39 (d, J = 7.8 Hz, 1H), 3.21 (bd, 1H), 2.93 (t, J = 7.8 Hz, 1H), 2.78 (dd, J = 3.6 & 7.8 Hz, 1H), 2.11 (s, 3H), 2.01 (s, 3H), 1.66 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 171.83, 170.84, 169.91, 168.03, 166.15, 165.43, 159.57, 154.17, 139.14, 138.85, 138.36, 134.08, 133.78, 132.66, 13.54, 129.67, 128.78, 128.43, 128.23, 127.78, 127.67, 127.56, 127.43, 127.23, 127.10, 117,53, 100.67, 100.32, 98.94, 97.18, 75.90, 78.31, 75.32, 74.95, 7.81, 74.43, 73.99, 73.58, 73.45, 73.33, 73.29, 73.23, 73.12, 69.90, 69.56, 68.66, 67.56, 58.70, 53.43, 21.28, 21.07, 20,98; ESI-MS: m/z calcd for C97H103Cl3N2O13; 1982.5562 found
1905.5558 (M + Na)+.
Figure imgf000115_0001
[00403] Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2- ulopyranosylonate-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→2)-O-3,4,6-tri-O-benzyl-α-D-mannopyranosyl fluoride (9): PdCl2 (0.050 g) was added to a solution of S4e (2.7 g, 1.42 mmol) in 20 mL of CH2Cl2: MeOH (1:1). The reaction mixture was stirred at room temperature for 5 h until TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of the starting material. The reaction mixture was then filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford 1-OH compound (2.0 g) as white color foam. The residue (2 g, 1.07 mmol) was dissolved in CH2Cl2 (10 mL) at - 30 oC, then DAST (284 μL, 2.14 mmol) was added slowly. The resulting reaction mixture was stirred for 1 h. When TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in toluene) to afford 9 (1.45 g, 55% over 2 steps) as white foam. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; 1H NMR (600 MHz, CDCl3): δ 7.96 (m, 4H), 7.55 (m, 2H), 7.40-7.17 (m, 34H), 5.86 (t, J = 10.2Hz, 1H), 5.50 (d, J = 52Hz, 1H), 5.44-5.40 (m, 2H), 5.29 (dd, J = 1.6 & 7.8 Hz, 1H), 5.15 (dd, J = 1.7 & 7.2 Hz, 1H), 5.05-4.99 (m, 2H), 4.84-4.44 (m, 10H), 4.33-4.20 (m, 3H), 4.27-4.20 (m, 4H), 4.03-3.90 (m, 3H), 3.72-3.65 (s, 3H), 3.70-3.06 (m, 12H), 3.46-3.30 (m, 1H), 3.00 (t, J = 10.2 Hz, 1H), 2.86 (dd, J = 3.2 & 12.3 Hz, 1H), 2.19 (s, 3H), 2.16 (s, 3H), 2.12 (t, J = 8.4 Hz, 1H), 2.0 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 170.8, 170.0, 168.0, 166.1, 165.2, 159.5, 154.1, 138.9, 138.4, 138.2, 138.1, 133.7, 133.6, 133.4, 130.0, 129.9, 129.6, 129.3, 128.8, 128.6, 128.5, 128.4, 128.3, 128.1, 127.9, 127.5, 127.2, 125.5, 107.7, 100.7, 100.1, 99.2, 95.8, 78.1, 77.1, 76.6, 75.3, 74.9, 74.6, 74.4, 74.1, 73.9, 73.7, 73.5, 73.3, 73.0, 72.6, 72.5, 69.2, 69.0, 67.3, 63.2, 61.8, 58.1, 57.3, 53.4, 37.3, 21.7, 21.3, 21.0, 20.9 ; ESI-MS: m/z calcd for C94H98Cl3FN2O29; 1844.5204 found 1867.5192 (M + Na)+.
[00404] Synthesis of building blocks 10 and 11.
[00405] Pentasaccharides S5a and S5b were obtained according to our previous report3, in which the functional group was further modified from N-pthallamide to N-Troc. Finally, the anomeric p-methoxy phenyl group was removed and resulting–OH was changed to fluoride in presence of DAST.
Figure imgf000117_0001
Figure imgf000117_0002
[00406] Scheme S5 | Preparation of compound 10 and 11. i, (1) EDA, n-BuOH, 90 oC; (2) Troc-Cl, NaHCO3, CH2Cl2; (3) Ac2O, pyridine; ii, (1) CAN, ACN: Toluene: H2O; (2) DAST, CH2Cl2,-30 oC.
[00407] General procedure for step i: A mixture of compound S5a and S5b (0.500 g, 0.212 mmole) and 10 mL of ethylene diamine: n-BuOH (1:4) was stirred at 90 oC overnight.
Volatiles were evaporated, and the crude product was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (0.114 g, 2.12 mmol) and 2,2,2-trichloro ethyl chloroformate (0.2 mL, 2.12 mmol) were added at 0 oC, allowed it to warm to RT and stirred for overnight. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material. The reaction mixture was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in toluene). The product was then acetylated using 10 mL of pyridine/acetic anhydride (6:4) until TLC indicated (ethyl acetate: toluene, 2/8) complete consumption of starting material. The reaction mixture was then concentrated in vacuo and purified by silica gel column chromatography (0%→ 15% EA in toluene) to afford S5c (0.332 g 65%) and S5d (0.340 g, 68%) as a colorless foam.
Figure imgf000118_0001
[00408] p-methoxyphenyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→2)-[2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→4)]-3,6-O-di-benzyl- α-D-mannopyranoside (S5c): Compounds S5c was prepared according to the above mentioned general procedure. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; 1H NMR (600 MHz, CDCl3): δ 7.40-7.08 (m, 50H, Ar-H), 6.92-6.72 (m, 10H, Ar-H), 6.63-6.53 (m, 2H, PMP-H), 5.31-5.24 (m, 2H'), 5.22 (d, J = 7.8 Hz, 1H), 5.15 (d, J = 8.4 Hz, 1H,), 4.94 (d, J = 3 Hz,), 4.88 (d, J = 3.6 Hz, 1H), 4.86 (d, J = 3.6 Hz, 1H), 4.80-4.71 (m, 7H), 4.64-4.56 (m, 3H), 4.49-4.44 (m, 10H,), 4.39-4.10 (m, 14H), 4.15-4.05 (m, 2H), 4.03 (t, J = 8.4 Hz, 1H), 3.98-3.86 (m, 3H), 3.79-3.72 (m, 1H), 3.69 (s, 3H), 3.58-3.56 (m, 1H), 3.49-3.25 (m, 13H), 3.08 (d, J = 8.4 Hz, 1H), 3.05 (d, J = 8.9 Hz, 1H), 2.90 (bs, 1H), 1.93 (s, 3H), 1.92 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.5, 169.4, 168.3, 167.8, 154.8, 150.3, 139.2, 139.1, 139.0, 138.9, 138.8, 138.5, 138.3, 138.2, 138.0, 134.0, 133.6, 132.1, 131.9, 131.7, 129.2, 128.6, 128.5, 128.3, 128.2, 128.1, 128.0, 127.9, 127.9, 127.8, 127.7, 127.6, 127.5, 127.4, 127.4, 127.3, 127.1, 127.0, 126.8, 123.5, 123.4, 123.3, 118.1, 114.4, 108.9, 100.9, 100.7, 98.5, 97.6, 97.1, 80.5, 50.5, 79.7, 77.9, 77.8, 77.7, 77.4, 77.2, 75.4, 74.9, 74.6, 74.5, 73.7, 73.6, 73.6, 73.4, 73.3, 73.0, 72.8, 72.7, 72.2, 71.9, 71.8, 71.7, 71.2, 69.2, 68.5, 68.3, 68.2, 67.6, 67.3, 56.4, 55.9, 55.7, 21.3, 21.2, 21.2; ESI-MS: m/z calcd for C131H138Cl6N2O31; 2449.7492; found 2449.7272 (M + H)+.
Figure imgf000119_0001
[00409] p-methoxyphenyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→2)-[2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→6)]-3,6-O-di-benzyl- α-D-mannopyranoside (S5d): Compounds S5d was prepared according to the above mentioned general procedure. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.61; 1H NMR (600 MHz, CDCl3): δ 7.42-7.05 (m, 60H), 7.02 (d, J = 9.2 Hz, 2H), 6.85 (d, J = 9.0 Hz, 2H), 5.59 (s, 1H), 5.42 (bs, 1H), 5.39-5.29 (m, 2H), 5.15 (d, J = 3.8 Hz, 1H), 5.00-4.84 (m, 7H), 4.80-4.25 (m, 20H), 4.10 (dd, J = 3.8 & 7.8 Hz, 2H), 4.00-3.83 (m, 6H), 3.76 (s, 3H), 3.62- 3.20 (m, 23H), 1.99 (s, 3H), 1.96 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.9, 169.5, 168.5, 155.0, 154.6, 150.1, 138.9, 138.4, 138.2, 138.1, 134.3, 132.0, 129.2, 128.6, 128.4, 128.3, 128.2, 128.1, 128.0, 127.9, 127.8, 127.6, 127.5, 127.3, 125.5, 123.6, 117.8, 117.2, 114.9, 106.1, 101.5, 100.9, 100.7, 98.3, 96.4, 95.7, 80.3, 80.1, 79.4, 78.3, 77.9, 78.3, 75.6, 74.8, 74.5, 74.4, 74.3, 73.6, 73.4, 73.2, 73.0, 72.6, 72.3, 71.8, 68.9, 68.1, 67.9, 67.5, 57.9, 56.7, 55.8, 41.3, 40.4, 37.7, 29.9, 21.6, 21.2, 21.1; ESI-MS: m/z calcd for C131H138Cl6N2O31; 2448.7492 found 2449.7414 (M + H) +.
[00410] General procedure for step ii: Cerium ammonium nitrate (0.616 g, 0.725 mmol) was added to a solution of compound S5c or S5d (0.350 g, 0.145 mmol) in 10 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at 0 °C for 2 h. The reaction was diluted with EtOAc (100 mL) and washed with H2O (30 x 2 mL) and brine (30 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by flash column chromatography (0%→ 15% EA in toluene) to afford 1-OH compound (0.180 m) as clear foam. The residue (0.180 g, 0.078 mmol) was dissolved in CH2Cl2 (10 mL) at -30 oC. Then, DAST (30 μL, 0.234 mmol) was added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (ethyl acetate: toluene, 1/9) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 8% EA in toluene) to afford 10 (0.120 g, 34% over 2 steps) and 11 (0.150 g, 42 % over 2 steps).
Figure imgf000120_0001
[00411] 2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→2)-[2-O-acetyl- 3,4,6-O-tri-benzyl-β-D-galacto-pyranosyl-(1→4)-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2- trichloroethoxy) carbonylamino-β-D-glucopyranosyl-(1→4)]-3,6-O-di-benzyl-α-D- mannopyranosyl fluoride (10): TLC (ethyl acetate: toluene =1/9, v/v): Rf = 0.34; 1H NMR (600 MHz, CDCl3): δ 7.34-7.13 (m, 60H), 5.41 (s, 1H), 5.50 (d, J = 51.1Hz, 1H), 5.30-5.25 (m, 2H), 5.12 (d, J = 8.4 Hz, 1H), 4.92-4.85 (m, 5H), 4.69-4.38 (m, 20H), 4.32-4.14 (m, 8H), 3.91-3.77 (m, 7H), 3.70 (dd, J = 3.8 and 7.8 Hz, 1H), 3.60-3.56 (m, 3H), 3.49-3.24 (m, 14H), 2.03 (s, 3H), 1.98 (s, 3H); 13C NMR (150 MHz, CHCl3): δ 169.68, 169.58, 154.31, 154.09, 139.06, 138.97, 138.93, 138.32, 138.29, 138.27, 138.20, 138.17, 129.32, 128.99, 128.69, 128.63, 128.50, 128.49, 128.45, 128.27, 128.24, 128.16, 128.15, 128.07, 128.05, 128.00, 127.97, 127.94, 127.91, 127.82, 127.72, 127.60, 127.57, 127.44, 125.58, 100.64, 100.45, 95.86, 80.54, 80.51, 76.81, 76.70, 76.03, 75.34, 75.08, 86, 74.77, 74.66, 74.57, 74.47, 73.74, 73.70, 73.67, 73.64, 73.58, 73.46, 73.42, 73.27, 72.90, 72.19, 72.17, 71.99, 71.95, 68.49, 68.27, 68.14, 68.01, 57.53, 21.40, 21.27; ESI-MS: m/z calcd for C124H131Cl6FN2O29; 2340.6953 found 2363.7200 (M + Na)+.
Figure imgf000121_0001
[00412] 2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→2)-[2-O-acetyl- 3,4,6-O-tri-benzyl-β-D-galacto-pyranosyl-(1→4)-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2- trichloroethoxy) carbonylamino-β-D-glucopyranosyl-(1→4)]-3,6-O-di-benzyl-α-D- mannopyranosyl fluoride (11): TLC (ethyl acetate: toluene =1/9, v/v): Rf = 0.38; 1H NMR (600 MHz, CDCl3): δ 7.33-7.09 (m, 60H), 5.60 (d, J = 52.1 Hz, 1H), 5.32-5.28 (m, 2H), 5.10 (d, J = 2.1 Hz, 1H), 4.93-4.80 (m, 5H), 4.78 (d, J = 8.4 Hz, 1H), 4.74 (d, J = 8.2 Hz, 1H), 4.65-4.40 (m, 28H), 3.95 (dd, J = 8.4 Hz, 1H), 3.79-3.69 (m, 10H), 3.50-3.40 (m, 4H), 3.39- 3.20 (m, 8H), 1.91 (s, 6H) ; 13C NMR (150 MHz, CHCl3): δ 169.69, 169.56, 154.72, 154.66, 139.55, 139.02, 139.00, 138.43, 138.34, 138.27, 138.20, 138.19, 128.93, 128.80, 128.76, 128.72, 128.65, 128.45, 128.41, 128.30, 128.28, 128.21, 127.67, 127.34, 127.10, 106.45, 105.33, 101.82, 101.21, 100.00, 97.86, 97.46, 95.60, 75.46, 75.27, 74.86, 74.58, 74.26, 74.10, 73.50, 73.47, 73.10, 72.90, 72.88, 72.37, 72.30, 71.40, 71.37, 71.09, 70.57, 70.35, 70.45, 69.78, 69.46, 29.99, 25.78, 22.87, 21.36, 21.29, 15.57, 14.49, 144.42; ESI-MS: m/z calcd for C124H131Cl6FN2O29; 2340.6953 found 2362.7225 (M + Na) +.
[00413] Synthesis of building blocks 12.
[00414] Preparation of disialylated antennae was commensed with β-1, 2 and β-1, 4 glycosylation of mannosyl acceptor S6a with donor S2b. Compound S6b was then modified to S6c and subsequently glycosylated with S4c to get desired heptasaccharide S6d. At last, the reducing end was modified to get donor 12.
Figure imgf000123_0001
Figure imgf000123_0002
[00415] Scheme S6 | Preparation of compound 12. i, NIS, TfOH, CH2Cl2, -50 oC, 76%; ii, (1) EDA, n-BuOH, 90 oC, (2) Troc-Cl, NaHCO3, CH2Cl2, 72% over 2 steps; iii, NIS, TfOH, CH2Cl2, -50 oC, 86%; iv, (1) CAN, ACN: Toluene: H2O, (2) DAST, CH2Cl2, -30 oC, 40% over 2 steps.
Figure imgf000123_0003
[00416] p-methoxyphenyl-O-4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- gluco pyranosyl-(1→2)-[4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranosyl-(1→4)]-3,6-O-di-benzyl-α-D-mannopyranoside (S6b): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S6a (0.560 g, 1.19 mmol) and donor S2b (1.74 g, 2.74 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at room temperature then cooled to -50 oC. NIS (1.07 g, 4.75 mmol) and TfOH (52 µL, 0.595 mmol) were added slowly, and the resulting reaction mixture was stirred for 2 h. When TLC (ethyl acetate: toluene, 1.5/8.5) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0% → 10% EA in toluene) to afford S6b (1.27 g, 76%) as clear foam. TLC (ethyl acetate : toluene = 1.5/8.5, v/v): Rf =0.57; 1H NMR (600 MHz, CDCl3): δ 7.66-7.16 (m, 18H), 6.97 (m, 12H), 6.66-6.49 (m, 4H), 5.25 (t, J = 10 Hz, 2H), 5.08-5.00 (dd, J = 9.6 & 3.4 Hz, 2H), 4.90 (d, J = 4.6 Hz, 1H), 4.69 (d, J = 12 Hz, 1H), 4.57 (t, 3H), 4.42-4.21 (m, 10H), 4.12 (dd, J = 3.2 & 8.4 Hz, 2H), 3.90 (dd, J = 3.2 & 7.8 Hz, 1H), 3.84-3.60 (m, 7H), 3.66 (s, 3H), 3.54- 3.31 (m, 7H), 3.01 (d, J = 7.8Hz, 1H), 1.84 (s, 3H), 1.80 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.61, 169.12, 154.49, 150.07, 138.69, 138.21, 137.99, 137.77, 137.60, 133.52, 131.29, 128.28, 128.19, 127.99, 127.94, 127.91, 127.83, 127.68, 127.59, 127.47, 127.25, 127.08, 127.94, 123.17, 117.55, 114.08, 98.10, 97.37, 96.54, 78.89, 74.56, 73.56, 73.27, 72.98, 72.42, 72.32, 71.91, 71.43, 71.02, 69.91, 69.25, 68.90, 55.73, 55.45, 55.26, 20.80; ESI-MS: m/z calcd for C77H82Cl6N2O21; 1585.3589 found 1586.5687 (M + H)+.
Figure imgf000125_0001
[00417] p-methoxyphenyl-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)
carbonylamino-β-D-glucopyranosyl-(1→2)-[3,6-O-di-benzyl-2-deoxy-2-(2,2,2- trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→4)]-3,6-O-di-benzyl-α-D- mannopyranoside (S6c): A mixture of compound S6b (1.9 g, 1.27 mmol) and 20 mL of ethylene diamine: n-BuOH (1:4) was stirred at 90 oC overnight. Volatiles were evaporated, and the crude product was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (0.687 g, 12.7 mmol) and 2,2,2-trichloro ethyl chloroformate (1.75 mL, 12.7 mmol) were added at 0 oC, allowed it to warm to rt and stirred for overnight until TLC (acetone: toluene, 1/9) indicated formation of product with consumption of starting material. The reaction mixture was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 8% EA in toluene) to afford S6c as a colorless solid (1.35 g, 72%). TLC (acetone: toluene = 1/9, v/v): Rf = 0.54; 1H NMR (600 MHz, CDCl3): δ 7.35-7.14 (m, 30H), 6.90 (d, J = 8.4 Hz, 2H), 6.79 (d, J = 8.6 Hz, 2H), 5.32 (d, J = 3.2 Hz, 1H), 5.27 (d, J = 7.2 Hz, 1H), 4.93 (d, J = 8.4 Hz, 1H), 4.73-4.58 (m, 10H), 4.48-4.43 (m, 7H), 4.19 (d, J = 7.2 Hz, 1H), 4.05-3.96 (m, 3H), 3.68 (s, 3H), 3.62-3.56 (m, 8H), 3.26 (q, 1H), 3.26-3.15 (m, 3H), 2.93 (m, 3H), 2.96 (s, 1H), 2.12 (s, 1H); 13C NMR (150 MHz, CDCl3): δ 155.26, 154.37, 154.27, 150.53, 138.93, 138.63, 138.48, 137.83, 137.74, 131.18, 128.96, 128.76, 128.67, 128.36, 128.21, 128.15, 127.89, 127.78, 118.00, 114, 85, 101.31, 98.79, 97.79, 95.81, 81.39, 79.59, 75.90, 74.70, 74.47, 74.01, 73.93, 73.53, 73.02, 72.83, 71.63, 71.37, 70.97, 68.99, 57.73, 57.40, 55.94 ; ESI-MS: m/z calcd for C73H78Cl6N2O19; 1499.3338 found 1499.3419.
Figure imgf000126_0001
[00418] p-methoxyphenyl-O-[Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero- α-D-galacto-non-2-ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galacto pyranosyl-(1→4)-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2-tri-chloroethoxy)carbonyl amino-β-D- glucopyranosyl-(1→2)-[Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D- galacto-non-2-ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galacto pyranosyl-(1→4)-O-3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranosyl-(1→4)-O-3,4,6-tri-O-benzyl-α-D-mannopyranoside (S6d): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S6c (0.500 g, 0.341 mmol) and donor S4c (0.772 g, 0.751 mmol) in anhydrous CH2Cl2 (10 mL) . The mixture was stirred for 1 h at rt and then cooled to -50 oC. NIS (0.383 g, 1.70 mmol) and TfOH (15 µL, 0.170 mmol) were added slowly. The resulting reaction mixture was stirred for 2 h. When TLC (acetone: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S6d (0.950 g, 86%) as clear foam. TLC (acetone: toluene = 2/8, v/v): Rf = 0.48; 1H NMR (600 MHz, CDCl3): δ 7.90-7.87 (m, 7H), 7.81-7.79 (m, 3H), 7.50-7.07 (m, 50H), 6.98 (d, 2H), 6.40 (d, 2H), 5.78-5.73 (m, 2H), 5.36-5.26 (m, 4H), 5.20 (d, J = 8.6 Hz, 1H), 5.19-5.15 (dd, J = 3.2 & 8.4 Hz, 2H), 5.05 (dd, J = 4.3 & 8.4 Hz, 2H), 4.94-4.78 (m, 4H), 4.68-4.15 (m, 30H), 3.96-3.86 (m, 6H), 3.71 (S, 6H), 3.70-3.59 (m, 15H), 3.57 (s, 3H), 3.34-3.26 (m, 5H), 2.98-2.76 (m, 4H), 2.15 (s, 3H), 2.09 (s, 3H), 2.00 (S, 3H), 1.98 (s, 3H), 1.89 (S, 3H), 1.89 (S, 3H); 13C NMR (150 MHz, CDCl3): δ 171.56, 170.89, 169.56, 167.20, 165.28, 165.00, 159.11, 154.79, 138.78, 138.56, 138.21, 137.29, 137.00, 133,67, 133.24, 130.79, 129.70, 129.60, 129.26, 128.78, 128.56, 128.42, 128.32, 128.11, 127.69, 127.56, 127.44, 127.32, 127.14, 117.78, 100.89, 100.56, 99.87, 99.68, 95.41, 79.13, 75.56, 74.18, 73.48, 73.26, 73.12, 71.00, 72.90, 72.78, 71.76, 68.78, 68.40, 68.42, 61.78, 57.78, 57.33, 55.89, 53.80, 38.90, 38.7, 30.98, 30.76, 28.87, 23.89, 22.65, 20.87, 20.65, 20.54, 14.08, 10.86; ESI-MS: m/z calcd for C161H168Cl6N4O55; 3251.8695 found 3251.8657 (M + Na)+.
Figure imgf000127_0001
[00419] [Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2- ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galacto pyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→2)-[Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2- ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→4)-O-3,4,6-tri-O-benzyl-α-D-mannopyranosyl fluoride (12): Cerium ammonium nitrate (0.470 g, 0.554 mmol) was added to a solution of compound S6d (0.300 g, 0.092 mmol) in 10 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at rt for 3 h. The reaction was diluted with EtOAc (100 mL) and washed with H2O (30 x 2 mL) and brine (30 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by flash column chromatography (0%→ 20% EA in toluene) to afford 1-OH compound (0.180 g) as a foam. The residue (0.180 g, 0.057 mmol) was dissolved in CH2Cl2 (10 mL) at -30 oC. Then, DAST (22 μL, 0.171 mmol) was added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (acetone: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 15% EA in toluene) to afford 13 (0.120 g, 41% over 2 steps) as white solid. TLC (acetone: toluene =2/8, v/v): Rf = 0.24; 1H NMR (600 MHz, CDCl3): δ 7.92-7.83 (m, 10H), 7.54-7.47 (m, 5H), 7.40-6.93 (m, 45H), 5.83 (m, 2H), 5.40-5.35 (m, 6H), 5.2 (dd, J = 3.2 & 7.8 Hz, 2H), 5.11 (dd, J = 4.3 & 8.4 Hz, 2H), 4.98-4.89 (m, 4H), 4.76-4.56 (m, 15H), 4.28-4.10 (m, 11H), 4.00-3.89 (m, 6H), 3.79-3.72 (m, 6H), 3.65 (s, 3H), 3.67 (s, 3H), 3.62-3.43 (m, 6H), 3.36-3.21 (m, 5H), 3.02- 2.98 (m, 4H), 2.16 (s, 3H), 2.14 (s, 3H), 2.11 (s, 3H), 2.06 (s, 3H), 2.01 (s, 3H), 1.98 (s, 3H), 1.89-1.76 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.80, 170.85, 170.06, 168.03, 166.12, 165.41, 159.56, 154.16, 138.75, 138.34, 133.73, 130.11, 129.94, 129.57, 129.19, 128.79, 128.72, 128.50, 128.38, 128.03, 127.75, 127.56, 100.69, 100.00, 96.67, 95, 78, 95.35, 95.12, 74.91, 74.65, 74.29, 73.00, 70.91, 69.01, 67.35, 61.87, 58.15, 57.60, 53.42, 37.17, 21.28, 20.97; ESI-MS: m/z calcd for C154H161Cl6FN4O53; 3147.6554 found 3169.8022 (M + Na)+.
[00420] Synthesis of building blocks 13.
[00421] Total chemical synthesis of partially sialylated antennae 13 is shown in scheme S7.
Figure imgf000129_0001
[00422] Scheme S7 | Preparation of compound 13. i, NIS, TfOH, CH2Cl2, -50 oC, 86%; ii, BH3.THF, Bu2BOTf, CH2Cl2, 65%; iii, NIS, TfOH, CH2Cl2, -50 oC, 76%; iv, (1) EDA, n- BuOH, 90 oC, (2) Troc-Cl, NaHCO3, CH2Cl2; (3) Ac2O, pyridine, 65% over 3 steps; v, Triethyl silane, TFA, CH2Cl2, 58%; vi, NIS, TfOH, CH2Cl2, -50 oC, 73%; vii, (1) CAN, ACN: Toluene: H2O, (2) DAST, CH2Cl2, -30 oC, 30% over 2 steps.
Figure imgf000129_0002
[00423] p-methoxyphenyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)-O-3,4-O-benzyl-α-D- mannopyranoside (S7c): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S7a (0.500 g, 1.07 mmol) and donor S7b (1.21 g, 1.28 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at room temperature then cooled to -50 oC. NIS (0.481 g, 2.14 mmol) and TMSOTf (48 µL, 0.267 mmol) were added slowly, and the resulting reaction mixture was stirred for 3 h. When TLC (ethyl acetate: toluene, 1/9) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S7c (1.30 g, 86%) as a pale yellow solid. TLC (ethyl acetate: toluene = 1/9, v/v): Rf = 0.59; 1H NMR (600 MHz, CDCl3): δ 7.75-7.65 (m, 4H), 7.37-7.15 (m, 30H), 6.98 (d, J = 8.1 Hz, 2H), 6.82 (d, J = 8.4 Hz, 3H), 6.70 (d, J = 8.4 Hz, 2H), 6.60 (d, J = 9.2 Hz, 2H), 5.39 (s, 1H), 5.34 (t, J = 10.2 Hz, 1H), 5.22 (dd, J = 7.2 & 2.8 Hz, 1H), 5.06 (d, J = 3.2 Hz, 1H), 4.89 (d, J = 11.4 Hz, 1H), 4.82 (d, J = 12.1 Hz, 1H), 4.75 (d, J = 11.8 Hz, 1H), 4.66-4.62 (m, 3H), 4.54-4.38 (m, 6H), 4.32 (d, J = 11.2 Hz, 1H), 4.29 (dd, J = 3.1 & 7.2 Hz, 2H), 4.27 (d, J = 10.8 Hz, 1H), 4.19 (t, J = 8.3 Hz, 1H), 4.00-3.89 (m, 4H), 3.72 (s, 3H), 3.58-3.33 (m, 8H), 3.0 (t, J = 8.7 Hz, 1H), 2.07 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.3, 154.9, 149.6, 138.8, 138.7, 138.6, 138.5, 138.1, 138.0, 137.9, 137.5, 133.6, 131.9, 128.7, 128.4, 128.4, 128.3, 128.2, 128.1, 128.1, 128.1, 128.0, 127.8, 127.8, 127.7, 127.7, 127.7, 127.6, 127.6, 127.5, 127.4, 127.3, 127.2, 126.8, 126.0, 123.0, 117.03, 114.5, 101.4, 100.9, 97.0, 96.2, 96.2, 80.3, 78.1,78.0, 75.6,74.9, 74.5, 74.4, 73.7, 73.4, 73.3, 72.6, 72.6, 72.0, 71.7, 71.3, 68.4, 68.1, 68.1, 64.2, 55.6, 55.6, 55.6, 21.0; ESI-MS: m/z calcd for C84H83NO19; 1409.5559 found 1432.5499 (M + Na)+.
Figure imgf000131_0001
[00424] p-methoxyphenyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)-O-3,4-O-dibenzyl-α-D- mannopyranoside (S7d): To a mixture of compound S7c (1.30 g, 1.02 mmol) and activated molecular sieves (1 g) in anhydrous CH2Cl2 (15 mL) was added borane.THF complex (0.978 mL of a 1M solution in THF, 10.2 mmol) and Bu2BOTf (0.439 mL of a 1M solution in CH2Cl2, 10.2 mmol) were added at 0 °C. The reaction mixture was allowed to stirred at room temperature for 4 h. TLC (acetone: toluene, 1/9) indicated formation of a product with consumption of the starting material. Triethyl amine was added to the reaction mixture followed by slow addition of methanol at 0 °C. When no more hydrogen was produced, the reaction mixture was filtered through Celite, the filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 7% EA in toluene) to afford S7d (0.850 g, 65%) as clear foam. TLC (acetone: toluene = 1/9, v/v): Rf = 0.31; 1H NMR (600 MHz, CDCl3): δ 7.84-7.66 (m, 4H), 7.42-7.02 (m, 30H), 7.03 (d, J = 8.4 Hz, 2H), 6.87 (t, J = 7.8 Hz, 3H), 6.67 (d, J = 12.1 Hz, 2H), 6.48 (d, J = 12.1 Hz, 2H), 5.39 (t, J = 10.2 Hz, 1H), 5.17 (d, J = 8.4 Hz, 1H), 4.93 (d, J = 12 Hz, 2H), 4.88 (d, J = 7.2 Hz, 1H), 4.85 (d, J = 12.1 Hz, 2H), 4.67 (dd, J = 4.3 & 8.4 Hz, 2H), 4.59-4.30 (m, 11H), 4.18 (t, J = 7.4 Hz, 1H), 4.01-3.96 (m, 3H), 3.84-3.78 (m, 3H), 3.76 (s, 3H), 3.68 (dd, J = 3.2 & 7.8 Hz, 1H), 3.54-3.34 (m, 6H), 3.25-3.20 (m, 1H), 2.01 (s, 3H) ; 13C NMR (150 MHz, CDCl3): δ 169.3, 167.9, 154.7, 149.6, 138.9, 138.7, 138.4, 138.2, 138.0, 138.0, 137.9, 134.1, 133.6, 131.9, 131.5, 129.0, 128.4, 128.4, 128.4, 128.3, 128.2, 128.2, 128.1, 128.1, 127.9, 127.8, 127.8, 127.7, 127.7, 127.7, 127.6, 127.6, 127.5, 127.3, 127.3, 126.8, 123.2, 123.0, 116.8, 114.4, 100.9, 97.6, 95.7, 80.3, 78.0, 76.9, 75.2, 75.1, 74.4, 74.4, 73.9, 73.6, 73.4, 73.3, 72.5, 72.3, 72.0, 71.6, 70.7, 68.6, 68.1, 62.2, 55.9, 55.6, 21.0; ESI-MS: m/z calcd for C84H85NO19; 1411.5716 found 1412.5726 (M + H)+.
Figure imgf000132_0001
[00425] p-methoxyphenyl-O-[2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl]-(1→2)-O-[3-O-benzyl-4,6-O- benzylidine-2-deoxy-2-phthalimido-β-D-glucopyranosyl]-(1→6)-3,4-O-dibenzyl-α-D- mannopyranoside (S7f): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S7d (0.600 g, 0.470 mmol) and donor S7e (0.557 g, 0.940 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at room temperature then cooled to -50 oC. NIS (0.211 g, 0.940 mmol) and TfOH (10.4 µL, 0.117 mmol) were added slowly, and the resulting reaction mixture was stirred for 2 h. When TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S7f (0.610g, 76%) as clear foam. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.49; 1H NMR (600 MHz, CDCl3): δ 7.66 (m, 8H), 7.38-7.15 (m, 29H), 7.10 (d, J = 8.4 Hz, 2H), 6.95-6.91 (m, 5H), 6.88-6.78 (m, 5H), 6.63 (d, J = 8.4 Hz, 2H), 6.50 (d, J = 8.8 Hz, 2H), 5.41 (s, 1H), 5.32 (t, J = 10.2 Hz, 1H), 5.11 (d, J = 8.4 Hz, 1H), 4.89 (d, J = 4.3 Hz, 1H), 4.87 (s, 1H), 4.80 (t, J = 8.8 Hz, 2H), 4.73 (s, 1H), 4.70 (s, 1H), 4.60 (t, J = 10.8 Hz, 3H), 4.57-4.40 (m, 5H), 4.35-4, 16 (m, 8H), 4.08 (t, J = 10.2 Hz, 1H), 4.00-3.89 (m, 4H), 3.85 (dd, J = 3.6 & 7.8 Hz, 1H), 3.78 (s, 3H), 3.70-3.61 (m, 3H), 3.52-3.41 (m, 4H), 3.40-3.28 (m, 4H), 3.20 (t, J = 10.2 Hz, 2H), 2.98 (m, 1H), 1.98 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 168.5, 164.8, 158.0, 153.0, 152.8, 151.6, 151.5, 150.6, 150.5, 149.2, 139.6, 138.9, 138.4, 138.1, 138.0, 137.4, 129.3, 129.2, 128.9, 128.9, 128.8, 128.9, 128.7, 128.5, 128.4, 128.2, 128.1, 128.0, 128.0, 127.9, 127.9, 127.7, 127.5, 127.4, 126.2, 125.5, 117.3, 114.9, 114.2, 102.2, 101.4, 100.9, 98.8, 96.5, 95.8, 95.7, 95.5, 95.3, 95.3, 95.0, 82.3, 80.6, 78.3, 76.2, 76.0, 75.8, 75.5,75.4, 75.2,74.9, 74.8,74.7, 74.7,74.2, 74.1, 73.8, 73.7, 73.5, 72.9, 72.3, 71.9, 68.9, 68.8, 68.2, 68.0, 66.4, 58.0, 57.1, 55.9, 44.3, 42.9, 40.8, 40.4, 40.3, 40.0, 21.7, 21.2; ESI-MS: m/z calcd for C111H108N2O24; 1882.7247 found 1882.7343.
Figure imgf000133_0001
[00426] p-methoxyphenyl-O-[2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl]- (1→2)-O-[3-O-benzyl-4,6-O-benzylidine-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranosyl]-(1→6)-3,4-O-dibenzyl-α-D-mannopyranoside (S7g): A mixture of compound S7f (0.950 g, 0.545 mmol) and 10 mL of ethylene diamine: n-BuOH (2:8) was stirred at 90 oC overnight. Volatiles were evaporated, and the crude product was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (0.363 g, 5.45 mmol) and 2,2,2-trichloro ethyl chloroformate (0.86 mL, 5.45 mmol) were added at 0 oC, allowed it to warm to rt and stirred for overnight. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material. The reaction mixture was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 10% EA in toluene). The product was then acetylated using 10 mL of pyridine/acetic anhydride (6:4) until TLC indicated (ethyl acetate: toluene, 2/8) complete consumption of starting material. The reaction mixture was then concentrated in vacuo and purified by silica gel column chromatography (0%→ 10% EA in toluene) to afford S7g as a white foam (0.650 g, 65%). TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; H NMR (600 MHz, CDCl3): δ 7.48 (d, J = 7.8 Hz, 2H), 7.39 (d, J = 8.2 Hz, 2H), 7.35- 7.12 (m, 41H), 6.91 (d, J = 10.2 Hz, 2H), 6.87 (d, J = 10.3 Hz, 2H), 5.55 (s, 1H), 5.50 (s, 1H), 5.32 (t, J = 10.2 Hz, 1H), 4.94-4.89 (m, 8H), 4.83-4.67 (m, 10H), 4.64-4.66 (m, 5H), 4.54- 4.50 (m, 3H), 4.36-4.22 (m, 6H), 4.06-3.87 (m, 6H), 3.83-3.46 (m, 10H), 3.38-3.34 (m, 3H), 3.20-3.10 (m, 2H), 2.33 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.5, 162.8, 155.0, 155.0, 154.8, 154.6, 154.51, 150.6, 150.5, 150.2, 139.6, 138.9, 138.4, 138.3, 138.3, 138.2, 138.1, 137.5, 129.3, 129.2, 128.7, 128.6, 128.6, 128.5, 128.5, 128.4, 128.3, 128.2, 128.1, 128.0, 128.0, 127.9, 127.9, 127.7, 127.5, 127.4, 126.2, 125.5, 117.3, 114.9, 114.2, 102.2, 101.4, 100.8, 98.3, 96.5, 95.8, 95.7, 95.5, 95.3, 95.3, 95.0, 82.3, 80.6, 78.3, 76.2, 76.0, 75.8, 75.5,75.4, 75.2,74.9, 74.8,74.7, 74.7,74.2, 74.1, 73.8, 73.7, 73.5, 72.9, 72.3, 71.9, 68.9, 68.8, 68.2, 68.0, 66.4, 58.0, 57.1, 55.9, 44.3, 42.9, 40.8, 40.4, 40.3, 40.0, 21.7, 21.2 ; ESI-MS: m/z calcd for C102H106Cl6N2O25; 1962.6590 found 1973.5278 (M + H)+.
Figure imgf000135_0001
[00427] p-methoxyphenyl-O-[2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl]- (1→2)-O-[3,6-O-dibenzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranosyl]-(1→6)-3,4-O-dibenzyl-α-D-mannopyranoside (S7h): To a solution of S7g (0.600 g, 0.328 mmol) in anhydrous CH2Cl2 (70 mL) was added triethyl silane (2.10 mL, 13.2 mmol) followed by trifluroacetic acid (0.953 mL, 13.2 mmol) at 0 oC. The resulting reaction mixture was stirred for 2 h. After 2 h, TLC (ethyl acetate: toluene, 1.5/8.5 v/v) indicated product formation with consumption of starting material. The reaction mixture was washed with sat. NaHCO3 (2 x 50 mL). The aqueous layer was further extracted with CH2Cl2 (3 x 30 mL), and the combined organic layer were washed with brine solution (100 mL), dried over MgSO4, filtered and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S7h (0.350 g, 58%) as clear oil. TLC (ethyl acetate: toluene = 1.5/8.5, v/v): Rf = 0.35; 1H NMR (600 MHz, CDCl3): δ 7.33-7.04 (m, 45H), 6.92 (d, J = 8.2 Hz, 2H), 6.80 (d, J = 8.3 Hz, 2H), 5.55 (s, 1H), 5.31 (t, J = 10.1 Hz, 1H), 5.06 (d, J = 3.2 Hz, 1H), 4.93-4.80 (m, 4H), 4.47-4.35 (m, 13H), 4.35-4.18 (m, 8H), 4.05 (dd, J = 3.2 & 7.8 Hz, 2H), 3.82 (d, J = 8.4 Hz, 2H), 3.80-3.62 (m, 14H), 3.49-3.20 (m, 6H), 3.10 (bs, 2H), 2.08 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 169.5, 168.0, 155.3, 155.0, 154.7, 150.2, 138.9, 138.4, 138.3, 138.2, 137.8, 132.7, 131.1, 129.0, 128.7, 128.7, 128.6, 128.6, 128.6, 128.5, 128.4, 128.3, 128.2, 128.1, 128.1, 128.0, 127.9, 127.8, 127.7, 127.5, 127.4, 117.3, 114.9, 101.5, 100.8, 95.7, 80.6, 78.5, 75.8,
75.3,74.9, 74.8, 74.6, 74.1, 74.0, 73.8, 73.7, 73.64, 73.5, 72.8, 72.3, 71.9, 71.1, 68.9, 68.8, 68.4, 68.2, 67.6, 58.0, 56.5, 55.9, 41.5, 39.0, 37.3, 33.7, 32.0, 31.4, 30.6, 29.9, 29.20, 26.6, 24.0, 23.2, 22.9, 21.2, 20.1, 14.6, 14.4, 14.3, 14.3, 11.2; ESI-MS: m/z calcd for
C102H108Cl6N2O25; 1974.6750 found 1975.5438 (M + H)+.
Figure imgf000136_0001
[00428] p-methoxyphenyl-O-[2-O-acetyl-3,4,6-O-benzyl-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→2)-[Methyl-5-acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2- ulopyranosylonate]-(2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galactopyranosyl-(1→4)-O- 3,6-O-di-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl- (1→6)-O-3,4,-di-O-benzyl-α-D-mannopyranoside (S7i): A mixture of donor S4c (0.187 g, 0.182 mmol), acceptor S7h (0.300 g, 0.151 mmol) and activated 4 Å molecular sieves (0.700 g) in dry CH2Cl2 (10 mL) was stirred at room temperature for 1 h. The reaction mixture was cooled to -50 oC, NIS (0.067 g, 0.302 mmol) and TfOH (4 µL, 0.037 mmol) were added slowly and resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite, extracted with saturated Na2S2O3 followed by NaHCO3, dried over sodium sulfate and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S7i (0.317 g, 73%) as colorless foam. TLC: (ethyl acetate: toluene = 1.5/8.5, v/v): Rf = 0.61; 1H NMR (600 MHz, CDCl3): δ 7.90 (m, 4H), 5.52-7.45 (m, 2H), 7.37-7.08 (m, 59H), 6.90 (d, J = 8.3 Hz, 2H), 6.80 (d, J = 8.3 Hz, 2H), 5.72 (t, J = 10.2 Hz, 1H), 5.53 (s, 1H), 5.35-5.32 (m, 3H), 5.20 (dd, J = 3.2 & 8.3 Hz, 1H), 5.08 (dd, J = 2.8 & 8.4 Hz, 2H), 4.99-4.79 (m, 7H), 4.70- 4.18 (m, 26H), 4.06 (dd, J = 3.2 & 7.8 Hz, 1H), 3.94 (m, 2H), 3.90-3.84 (m, 10H), 3.74 (s, 3H), 2.60 (s, 3H), 2.59-2.57 (m, 3H), 3.45-3.32 (m, 6H), 3.20 (t, J = 9.8 Hz, 1H), 2.90 (t, J = 10.2 Hz, 2H), 2.83 (dd, J = 3.2 & 7.8 Hz, 1H), 2.08 (s, 3H), 2.06 (s, 3H), 2.02 (t, J = 10.1 Hz, 1H), 1.99 (s, 3H), 1.91 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 171.4, 170.5, 169.7, 169.1, 167.4, 165.7, 165.1, 159.1, 154.6, 159.8, 138.5, 138.2, 138.1, 137.9, 137.4, 133.3, 133.1, 132.3, 130.2, 129.8, 129.6, 129.4, 128.7, 128.5, 128.4, 128.1, 127.9, 127.5, 127.4, 127.1, 127.08, 116.9, 114.5, 101.3, 100.6, 100.4, 100.0, 95.3, 80.2, 79.9, 77.4, 75.5, 75.3, 74.5, 74.3, 74.1, 73.7, 73.4, 73.2, 73.1, 72.5, 72.1, 71.5, 71.2, 70.8, 68.6, 68.5, 68.3, 67.8, 67.5, 67.3, 63.1, 61.5, 57.8, 56.6, 55.5, 53.1, 38.6, 37.0, 36.8, 33.3, 32.0, 31.0, 30.9, 28.8, 26.2, 25.5, 23.6, 22.8, 22.5, 20.8, 20.6, 19.7, 14.3, 13.9, 10.8; ESI-MS: m/z calcd for
C146H153Cl6N3O43; 2850.5080 found 2850.8248.
Figure imgf000137_0001
[00429] [2-O-acetyl-3,4,6-O-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl-(1→2)-[Methyl-5- acetamido-7,8,9-tri-O-acetyl-3,5-dideoxy-D-glycero-α-D-galacto-non-2-ulopyranosylonate]- (2→6)-4-O-benzyl-2,3-di-O-benzoyl-1-β-D-galactopyranosyl-(1→4)-O-3,6-O-di-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy) carbonylamino-β-D-glucopyranosyl-(1→6)-O-3,4,-di-O- benzyl-α-D-mannopyranosyl fluoride (13): To a solution of compound S7i (0.430 g, 0.150 mmol) in 10 mL of acetonitrile: toluene: H2O (4:2:1) was added cerium ammonium nitrate (0.641 g, 0.754 mmol) and the resulting reaction mixture was stirred at 0 °C for 2 h. The reaction was diluted with EtOAc (100 mL) and washed with H2O (30 x 2 mL) and brine (30 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by flash column chromatography (0%→ 20% EA in toluene) to afford 1-OH compound (0.240 g, 57%) as clear foam. The residue (0.200 g, 0.072 mmol) was dissolved in CH2Cl2 (10 mL) at -30 °C. Then, DAST (29 μL, 0.216 mmol) was added slowly, and the resulting reaction mixture was stirred for 2 h. When TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 10% EA in toluene) to afford 13 (0.104 g, 50%) as white foam. TLC (ethyl acetate: toluene =2/8, v/v): Rf = 0.44; 1H NMR (600 MHz, CDCl3): δ 7.95-7.90 (m, 4H), 7.58-7.49 (m, 2H), 7.39-7.18 (m, 59H), 5.82 (t, J = 10.2Hz, 1H), 5.65 (d, J = 51 Hz, 1H), 5.34 (t, J = 10.2 Hz, 2H), 5.21 (dd, J = 3.6 & 7.8 Hz, 1H), 5.13-4.19 (m, 30H), 4.10-4.09 (m, 5H), 4.02-3.74 (m, 12H), 3.65 (s, 3H), 3.64-3.27 (m, 14H), 3.02 (t, J = 10.2 Hz, 2H), 2.87 (dd, J = 3.2 & 7.8 Hz, 1H), 2.12 (s, 3H), 2.10 (s, 3H), 2.09 (t, J = 10.2 Hz, 1H), 2.00 (s, 3H), 1.97 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 171.4, 170.2, 169.7, 169.1, 167.4, 165.6, 165.1, 159.1, 154.4, 139.0, 138.8, 138.2, 138.1, 138.0, 137.7, 133.3, 129.8, 129.7, 129.2, 128.7, 128.4, 128.1, 127.9, 127.7, 127.6, 127.5, 127.4, 127.3, 127, 1, 127.0, 125.2, 101.4, 100.7, 100.4, 9.9, 97.3, 95.180.2, 79.6, 78.6, 75.5, 74.5, 74.3, 73.8, 73.5, 73.3, 73.1, 72.8, 71.3, 71.3, 70.7, 70.1, 68.6, 67.8, 66.9, 63.1, 61.5, 57.8, 53.1, 37.1, 25.5, 21.3, 20.9, 20.5; ESI-MS: m/z calcd for
C139H146Cl6FN3O41; 2746.3454 found 2746.7604.
[00430] Preparation of core trisaccharides 14-15 S
[00431] The reducing end trisaccharide (Man-β-1,4-GlcNAc-β-1,4-GlcNAc-β-linker) 14 with N-pthallamide protections was obtained according to our previous report3. Compound 14 was next modified to 15 as shown in scheme S8.
Figure imgf000139_0001
Figure imgf000139_0002
[00432] Scheme S8 | Preparation of compound 15. i, (1) EDA, n-BuOH, 90 °C, (2) Troc-Cl, NaHCO3, CH2Cl2, 72% over 2 steps; ii, Ac2O, pyridine, 79%; iii, DDQ, CH2Cl2 H2O, 58%.
Figure imgf000139_0003
[00433] 5-Azidopentyl-O-2-O-acetyl-3-O-p-methoxy-benzyl-4,6-O-benzylidine-β-D-manno- pyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)
carbonylamino-β-D-glucopyranoside (S8b): A mixture of compound S8a (0.950 g, 0.545 mmol) and 10 mL of ethylene diamine: n-BuOH (2:8) was stirred at 90 °C overnight.
Volatiles were evaporated, and the crude mixture was dried using high vacuum. It was then dissolved in CH2Cl2 (20 mL), NaHCO3 (0.363 g, 5.45 mmol) and 2,2,2-trichloro ethyl chloroformate (0.86 mL, 5.45 mmol) were added at 0 °C, allowed it to warm to rt and stirred for overnight. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material. Reaction was diluted with CH2Cl2 (100 mL), washed with water (2 x 50 mL) and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 10% EA in toluene). The product was then acetylated using 10 mL of pyridine/acetic anhydride (6:4) until TLC indicated (ethyl acetate: toluene, 2/8) complete consumption of starting material. The reaction mixture was then concentrated in vacuo and purified by silica gel column chromatography (0%→ 10% EA in toluene) to afford S8b as a white foam (0.650 g, 65%). TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.64; 1H NMR (600MHz, CDCl3): δ 7.62-7.20 (m, 34H), 5.89 (s, 1H), 4.56 (d, J = 3.2 Hz, 1H), 4.23 (d, J = 8.9 Hz, 2H), 4.20-4.10 (m, 12H), 4.00-3.86 (m, 5H), 3.69-3.30 (m, 14H), 3.29 (s, 3H), 3.22-3.20 (m, 4H), 3.20-3.00 (m, 1H), 2.66 (s, 3H, -C(O)CH3, 1.56-1.38 (m, 4H, -CCH2C-, linker), 1.21-1.23(m, 2H, - CCH2C-, linker) ; 13C NMR (150 MHz, CDCl3): δ 177.7, 169.6, 167.0, 138.5, 138.4, 138.3, 138.2, 137.2, 137.8, 137.5, 134.2, 133.2, 133.6, 131.7, 131.1, 131.45, 129.8, 129.06, 128.9, 128.2, 128.4, 128.2, 128.4, 128.7, 127.8, 127.87, 127.83, 127.4, 127.4, 127.0, 127.2, 127.29, 127.6, 127.20, 126.88, 126.24, 125.1, 123.6, 123.3, 101.5, 102.7, 99.7, 98.0, 97.1, 78.13, 78.55, 78.05, 75.82, 74.57, 75.38, 75.27,74.25, 74.30, 72.78, 72.26, 70.89, 66.85, 68,43, 68.25, 67.75, 66.87, 55.57, 53.71, 52.10, 28.97, 28.87, 23.80, 22.77, 20.12; ESI-MS: m/z calcd for C74H83Cl6N5O20: 1575.1930 ; found 1576.235 (M + H)+.
Figure imgf000140_0001
[00434] 5-Azidopentyl-O-2-O-acetyl-4,6-O-benzylidine-β-D-mannopyranosyl-(1→4)-O- (3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl)- (1→4)-O-3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranoside (15): To a solution of S8a (1.0 g, 0.673 mmol) in 10 mL (CH2Cl2 : H2O, 10/1) was added DDQ (0.183 g, 0.808 mmol) at 0 °C and the resulting reaction mixture was stirred until TLC (ethyl acetate: toluene, 2/8) indicated formation of a product with consumption of the starting material. The reaction mixture was then filtered and the organic layer washed with H2O (2 x 30 mL). The aqueous layer was further extracted with CH2Cl2 (2 x 50 mL). The combined organic layers were washed with brine solution (40 mL), dried over Na2SO4, and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford 15 (0.652 g, 70%) as colorless foam. TLC (ethyl acetate: toluene =2/8 v/v): Rf = 0.24; 1H NMR (600 MHz, CDCl3): δ 7.44-7.16 (m, 30H), 5.44 (s, 1H), 5.15 (d, J = 3.2 Hz, 1H), 4.88 (t, J = 8.9 Hz, 2H), 4.54-4.40 (m, 12H), 4.08-3.58 (m, 3H), 3.56-3.40 (m, 14H), 3.25-3.20 (m, 4H), 3.02-3.00 (m, 1H), 2.16 (s, 3H, - C(O)CH3, 1.51-1.47 (m, 4H, -CCH2C-, linker), 1.30-0.99 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 171.5, 168.6, 167.0, 138.7, 138.4, 138.38, 138.2, 137.2, 137.8, 137.5, 134.2, 133.2, 133.6, 131.7, 131.1, 131.45, 129.8, 129.06, 128.9, 128.2, 128.4, 128.2, 128.4, 128.7, 127.8, 127.87, 127.83, 127.4, 127.4, 127.0, 127.2, 127.29, 127.6, 127.20, 126.88, 126.24, 125.1, 123.6, 123.3, 101.5, 102.7, 99.7, 98.0, 97.1, 78.13, 78.55, 78.05, 75.82, 74.57, 74.37, 74.27,73.25, 73.30, 72.78, 71.26, 69.89, 68.85, 69,43, 68.25, 67.73, 66.67, 56.57, 55.71, 51.10, 28.67, 28.27, 23.00, 21.47, 21.02 ; ESI-MS: m/z calcd for C66H75Cl6N5O19: 1455.0420; found 1476.3082 (M + Na)+.
[00435] Synthesis of high-mannose type oligosaccharides (G1-G6) S
Figure imgf000142_0001
Figure S1 | Structures of high mannose type glycans and their fragments [00436] With the donors 1-5 in hand, we investigated their glycosylation with core trisaccharide acceptor 14 and the coupling products (Scheme S9). The glycosylation of 14 with known imidate donor 1 to give tetrasaccharide S9a in 70% yield11. After selective benzylidene ring opening of S9a, the resulting 6”-OH S9b was glycosylated with 1 to afford the desired fully protected Man3GlcNAc2 pentasaccharide S9d, an early intermediate in N- Glycan biosynthesis and thus a conserved motif in all N-glycans, in 60% yield. In another pathway, reductive opening of the benzylidene group S9a resulted in diol S9c, which was further condensed with trimannosyl fluoride 4 by using Cp2HfCl2 and AgOTf to obtain heptasaccharide S9e, an intermediate in GlcNAc mediated branching in the Golgi apparatus, in 52% yield11.
Figure imgf000143_0001
[00437] Scheme S9 | Preparation of Man3 and Man5GlcNAc2. a, BF3.OEt2, CH2Cl2, 4 Å MS, -40 °C, 2 h, 70%; b, Triethyl silane, PhBCl2, CH2Cl2, 4 Å MS, -78 °C, 1 h, 82%; c, 1, BF3.OEt2, CH2Cl2, 4 Å MS, -60 °C to -20 °C, 2 h, 60%; d, pTsOH, CH3CN, 2 h, 66%; e, 4, AgOTf, Cp2HfCl2, Toluene, 4 Å MS, -40 °C, 2 h, 52%; f, (1) NH2CH2CH2NH2, nBuOH, 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2; G1: 65%; G2: 52%; G4: 29%; Cp2HfCl2: Bis
(cyclopentadienyl) hafnium Dichloride. To synthesize Man9GlcNAc2, a major glycoform found on HIV-1 gp120 surface and an important component of epitope recognized by broadly neutralizing antibodies, compound 14 was subjected to 3”-O glycosylation with fluoride 2 under the promotion of Cp2HfCl2/AgOTf to get hexasaccharide S10a in 65% yield. The p- toluene sulfonic acid mediated reductive ring opening of S10a provided diol S10b, which was further glycosylated with 5 to afford undecasaccharide S10c (Scheme S10).
Figure imgf000145_0001
00438 Scheme S10 Pre aration of Man4 G5 and Man9GlcNAc2 G6. a 2 AOTf
Figure imgf000145_0002
nBuOH, 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2; G5:42%; SG6: 26%; (BrC6H4)3NSbCl6: Tris (4- bromophenyl) ammoniumyl hexachloroantimonate.
Figure imgf000146_0001
[00439] 5-Aminopentyl-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G1): Compound 14 (0.150 g, 0.110 mmol) was deprotected by following general procedure 2 (Method 1) to yield desired trisaccharide G1 (0.045 g, 65%) as a white solid. 1H NMR (600 MHz, D2O): δ 4.72 (S, 1H, overlapped with D2O, H-1c), 4.60 (d, J = 7.8 Hz, 1H, H-1a), 4.49 (d, J = 7.8 Hz, 1H, H-1b), 4.06 (d, J = 3 Hz, 1H), 3.94-3.89 (m, 4H), 3.86-3.58 (m, 14H), 3.50-3.49 (m, 1H), 3.42-3.42 (m, 1H), 2.97 (t, J = 10.8 Hz, 2H, -CH2NH2, linker), 2.07 (s, 3H, -C(O)CH3), 2.03 (s, 3H, -C(O)CH3), 1.68-1.65 (m, 2H, -CCH2C-, linker), 1.60-1.58 (m, 2H, -CCH2C-, linker), 1.40-1.39 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 177.32, 177.17, 173.76, 104.12 (C-1a, 1 J C,H = 163.1), 103.80 (C-1b, 1 J C,H = 162.2), 102.80 (C-1c, 1 J C,H = 160.2), 82.07, 81.35, 79.15, 77.31, 77.25, 75.49, 75.13, 74.68, 73.23, 72.84, 69.34, 63.65, 62.83, 62.77, 57.75, 57.72, 42.05, 30.78, 29.10, 24.86, 24.84, 24.83; ESI-MS: m/z calcd for C27H49N3O16: 671.3005; found 694.3115 (M + Na)+.
Figure imgf000146_0002
[00440] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O- acetyl-4,6-O-benzylidine-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2- phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- gluco-pyranoside (S91): A mixture of trichloroacetimidate 1 (0.278 g, 0.437 mmol), chitobiose acceptor 14 (0.300 g, 0.219 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at room temperature for 1 h. The reaction was cooled to -40 °C, boron trifluoride ethyl etherate (12 µL, 0.109 mmol) was then added slowly and the resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→15% EA in toluene) to afford S9a (0.310 g, 70%) as white foam. TLC (ethyl acetate: toluene = 2/8, v/v): Rf = 0.46; 1H NMR (600 MHz, CDCl3): δ 7.84-7.65 (m, 8H, Ar-H), 7.38-7.31 (m, 2H, Ar-H), 7.30-7.18 (m, 28H, Ar-H), 6.98-6.90 (m, 7H, Ar-H), 6.75-6.71 (m, 3H, Ar-H), 5.45 (s, 1H, Ph-CH, benzylidene), 5.43- 5.43 (d, J = 3.4 Hz, 1H, H-2d), 5.34 (d, J = 3.1 Hz, 1H, H-2c), 5.21 (d, J = 8.1 Hz, 1H, H-1a), 5.19 (d, J = 2.1 Hz, 1H, H-1d), 4.90 (d, J = 8.1 Hz, 1H, H-1a), 4.83-4.81 (m, 3H), 4.67 (s, 1H), 4.67-4.61 (m, 2H), 4.53-4.43 (m, 7H), 4.38-4.23 (q, 2H), 4.22-4.16 (m, 1H), 4.13-4.06 (m, 6H), 3.87-3.75 (m, 6H), 3.66-3.60 (m, 3H), 3.53-3.45 (m, 3H), 3.38 (dd, J = 4.2 & 12.0 Hz, 1H), 3.26-3.17 (m, 3H), 3.09-3.07 (m, 1H), 2.87-2.82 (m, 2H), 2.06 (s, 3H, -C(O)CH3), 2.03 (s, 3H, -C(O)CH3), 1.35-1.23 (m, 4H, -CCH2C-, linker), 1.07-1.01 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 169.87, 168.75, 167.83, 138.97, 138.47, 138.17, 137.36, 134.30, 134.10, 131.72, 129.12, 128.90, 128.64, 128.55, 128.51, 128.32, 128.23, 128.09, 127.84, 127.46, 128.14, 126.24, 123.40, 101.44, 99.38, 98.90, 98.37 (C-1d, 1 J C,H = 172 Hz), 97.31, 79.05, 78.84, 77.89, 76.14,75.02, 74.78, 73.70, 73.40, 73.06, 73.04, 72.37, 72.03, 71.00, 69.11, 69.85, 69.11, 68.85, 68.59.68.50, 67.84, 66.70, 56.85, 55.99, 51.38, 28.95, 28.55, 23.28, 21.33, 21.16; ESI-MS: m/z calcd for C105H107N5O25: 1838.7180; found 1861.7223 (M + Na)+.
Figure imgf000148_0001
[00441] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O- acetyl-4-O-benzyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido- β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranoside (S9b): A mixture of tetrasaccharide S9a (0.280 g, 0.152 mmol) and 4 Å activated molecular sieves in CH2Cl2 (10 mL) was stirred at room temperature for 1 h. Reaction was cooled to -78 °C, triethyl silane (73 µL, 0.456 mmol) and dichlorophenyl borane (69 µL, 0.532 mmol) were added and stirred for 1 h. The reaction was quenched by adding Et3N, filtered through Celite and concentrated in vacuo. The residue was co-distilled with methanol 2-3 times before being purified by flash column chromatography (0%→ 15% EA in toluene) to afford 6”-OH S9b (0.230 g, 82%). TLC: (ethyl acetate: toluene =2/8, v/v): Rf = 0.36; 1H NMR (600 MHz, CDCl3): δ 7.85-7.52 (m, 8H, Ar-H), 7.52-7.12 (m, 29H, Ar- H), 7.00-6.88 (m, 9H, Ar-H), 6.74-6.70 (m, 3H, Ar-H), 5.39 (d, J = 1.8 Hz, 1H, H-2d), 5.32 (d, J = 3.6 Hz, 1H, H-2c), 5.21 (d, J = 8.4 Hz, 1H, H-1a), 5.10 (s, 1H, H-1d), 4.90-4.81 (m, 4H), 4.67-4.61 (m, 2H, overlapped H-2b), 4.59 (s, 1H, H- 1c), 4.59-4.44 (m, 9H), 4.37(d, J = 12 Hz, 2H), 4.24-4.12 (m, 3H), 4.10-4.05 (m, 3H), 3.90-3.77 (m, 4H), 3.69-3.58 (m, 7H), 3.49 (t, J = 11.5 Hz, 2H), 3.41-3.36 (dd, J = 6.1, 11.2 Hz, 2H), 3.26 (dd, J = 6.0, 9.2 Hz, 1H), 3.26-3.18 (m, 2H), 3.06-2.98 (m, 1H), 2.88-2.81 (m, 2H, linker), 2.06 (s, 3H, -C(O)CH3), 2.04 (s, 3H, -C(O)CH3), 1.37-1.22 (m, 4H, linker), 1.07 -1.00 (m, 2H, linker); 13C NMR (150 MHz, CDCl3): δ 170.45, 169.88, 168.78, 168.24, 167.86, 138.95, 138.92, 138.77, 138.58, 138.21, 138.11, 137.95, 137.37, 134.35, 134.16, 133.89, 132.09, 131.70, 128.90, 128.76, 128.71, 128.64, 128.58, 128.51, 128.41, 128.31, 128.08, 127.96, 127.81, 127.64, 127.13, 123.97, 123.46, 100.14, 98.40, 98.36, 97.36, 76.24, 75.52, 75.30, 74.96, 74.71, 74.51, 74.29, 73.41, 73.09, 72.55, 72.12, 69.41,69.20, 68.85, 68.48, 67.93, 67.71, 61.87, 56.78, 56.00, 51.38, 28.96, 28.55, 23.28, 21.37; ESI-MS: m/z calcd for C105H109N5O25:
1840.7337; found 1863.7383 (M + Na)+.
Figure imgf000149_0001
[00442] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O- acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S9c): p- Toluenesulfonic acid monohydrate (0.045 g, 0.239 mmol) was added to a stirred solution of tetrasaccharide S9a (0.220 g, 0.119 mmol) in acetonitrile (10 mL) at room temperature. After 8 h, the reaction mixture was quenched with Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to give the title diol S9c (0.140 g, 66%) as white solid. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.26; 1H NMR (600 MHz, CDCl3): δ 7.85-7.52 (m, 8H, Ar-H), 7.32-7.17 (m, 25H, Ar-H), 6.98- 6.91 (m, 7H, Ar-H), 6.75-6.71 (m, 3H, Ar-H), 5.30 (d, J = 3.6 Hz, 1H, ), 5.21(d, J = 8.6 Hz, 1H, H-1a ), 5.20 (s, 2H, overlapped H-1d), 4.89 (d, J = 8.4 Hz, 1H, H-1b), 4.85-4.82 (m, 3H), 4.64-4.60 (m, 3H), 4.544.46 (m, 7H), 4.38 (d, J = 12.0 Hz, 1H), 4.34 (d, J = 12.2 Hz, 1H), 4.21-4.04 (m, 5H), 3.92 (m, 1H), 3.87-3.79 (m, 3H), 3.70-3.59 (m, 5H), 3.52-3.43 (m, 4H), 3.39 (dd, J = 3.2, 8.3 Hz, 1H), 3.28 (dd, J = 3.2, 8.2 Hz, 1H), 3.29-3.19 (m, 2H), 2.29 (m, 1H), 2.86-2.83 (m, 3H), 2.11 (s, 3H, -C(O)CH3), 2.03 (s, 3H, -C(O)CH3), 1.35-1.23 (m, 4H, -CCH2C-, linker), 1.06-1.01 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.76, 169.88, 138.92, 138.70, 138.62, 138.52, 138.12, 138.06, 134.27, 134.07, 133.81, 131.95, 131.64, 128.82, 128.64, 128.59, 128.52, 128.50, 128.39, 138.33, 128.20, 128.09, 128.06, 128.03, 128.01, 127.94, 127.81, 127.75, 127.54, 127.42, 127.29, 127.06, 123.90, 123.36, 98.51, 98.30, 98.24(C-1d, 1 J, C,H = 173 Hz), 97.30, 79.07, 78.38, 77.60, 76.10, 75.52, 75.03, 74.79, 74.71, 74.59, 74.51, 73.39, 73.03, 72.07, 72.01, 71.30, 69.53, 69.27, 69.05, 68.44, 67.70, 67.17, 62.44, 56.74, 55.94, 51.32, 28.89, 28.49, 23.22, 21.31, 21.22; ESI-MS: m/z calcd for C98H103N5O25: 1750.6868; found 1773.6913 (M + Na)+.
Figure imgf000150_0001
[00443] 5-Azidopentyl-O-di-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3), (1→6)-2-O-acetyl-4-O-benzyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2- phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranoside (S9d): A mixture of donor 1 (0.113 g, 0.178mmol), acceptor S9b(0.220 g, 0.119 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at room temperature for 1 h. The reaction was cooled to -60 °C, boron trifluoride ethyl etherate (12 µL, 0.109 mmol) was added slowly and the resulting reaction mixture was stirred for 2 h at - 20 °C. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 20% EA in hexane) to afford S9d (0.170 g, 60%) as colorless foam. TLC: (ethyl acetate: hexane = 3/7, v/v): Rf = 0.46; 1H NMR (600 MHz, CDCl3): δ 7.77-7.59 (m, 8H, Ar- H), 7.32-7.16 (m, 43H, Ar-H), 7.14-7.08 (m, 2H, Ar-H), 6.91-6.89 (m, 4H, Ar-H), 6.73-6.67 (m, 6H, Ar-H), 5.45 (s, 1H, H-2d), 5.34 (d, J = 3.1 Hz, 1H, H-2c), 5.32 (s, 1H, H-2d'),5.17 (d, J = 8.4 Hz, 1H, H-1a), 5.09 (s, 1H, H-1d), 5.0 (s, 1H, H-1d'), 4.87 (d, J = 8.4 Hz, 1H, H-1b), 4.83-4.78 (q, 2H), 4.74-4.71 (q, 2H), 4.65-4.61 (m, 4H), 4.56-4.42 (m, 15H), 4.31 (d, J = 9.2 Hz, 1H), 4.12-4.03 (m, 5H), 4.03-3.76 (m, 9H), 3.68-3.43 (m, 9H), 3.30 (dd, J = 3.2, 9.1 Hz, 1H), 3.21-3.15 (m, 2H), 3.13 (d, J = 9.2 Hz, 1H), 3.09 (d, J = 8.4 Hz, 1H), 2.89-2.79 (m, 2H, - CH2N3-, linker), 2.12 (s, 3H, -C(O)CH3), 2.07 (s, 3H, -C(O)CH3), 1.69 (s, 3H, -C(O)CH3), 1.37-1.12 (m, 4H, -CCH2C-, linker), 1.07-1.01 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.45, 170.22, 170.18, 168.21, 167.71, 138.93, 138.72, 138.68, 138.50, 138.24, 138.22, 138.07, 133.83, 133.75, 128.87, 128.79, 128.67, 128.63, 128.58, 128.42, 128.21, 128.06, 127.99, 127.96, 127.81, 127.76, 127.70, 127.46, 127.08, 123.36, 100.13 (C- 1a, 1 J C,H = 159.3 Hz), 99.39 (C-1d', 1 J C,H = 171.5 Hz), 98.35 (C-1b, 1 J C,H = 162.3 Hz), 98.31(C-1d, 1 J C,H = 170 Hz), 97.16, 76.20, 76.05, 75.58, 75.21, 74.97, 74.89, 74.70, 74.47, 74.28, 73.94, 73.72, 73.00, 72.25,72.20, 71.70,71.50, 69.15,69.07, 69.04,68.99, 68.50, 68.45, 67.80, 65.45, 56.83, 51.37, 29.94, 23.27, 21.31, 21.28, 20.83; ESI-MS: m/z calcd for C134H139N5O31: 2314.9379; found 2337.9461 (M + Na)+.
Figure imgf000151_0001
[00444] 5-Aminopentyl-di-(α-D-mannopyranosyl)-(1→3),(1→6)-β-D-mannopyranosyl- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-gluco- pyranoside (G2): Pentasaccharide S9d (0.090 g, 0.038 mmol) was deprotected by following the general procedure 2 (Method 1) to afford compound G2 (0.020 g, 52%) as a white powder. 1H NMR (600 MHz, D2O): δ 5.10 (d, J = 1.3 Hz, 1H, H-1d), 5.09 (d, J = 1.5 Hz, 1H, H-1d'), 4.78 (s, 1H, overlapped with D2O, H-1c), 4.59 (d, J = 8.4 Hz, 1H, H-1a), 4.49 (d, J = 7.8 Hz, 1H, H-1b), 4.25 (s, 1H), 4.01 (d, J = 1.5 Hz, 1H), 4.00 (d, J = 1.3 Hz, 1H), 3.97- 3.77 (m, 8H), 3.75-3.65 (m, 20H), 3.52-3.48 (m, 2H), 2.98 (t, J = 11.2 Hz, 2H), 2.06 (s, 3H),2.02 (s, 3H), 1.68-1.65 (m, 2H), 1.601.57 (m, 2H), 1.49-1.40 (m, 2H); 13C NMR (150 MHz, D2O): δ 181.17, 174.69, 174.42, 102.51 (C-1d, 1 J C,H = 171.5 Hz), 101.34, 101.04, 100.35 (C-1d', 1 J C,H = 173.5 Hz), 99.60, 80.48, 79.61, 79.30, 74.49, 74.36, 74.16, 73.43, 72.66, 72.37, 71.93, 70.39, 70.31, 70.13, 70.09, 69.98, 69.85, 66.84, 66.76, 65.80, 61.12, 90.93, 60.07, 59.97, 54.97, 54.85, 39.30, 28.03, 26.35, 23.07, 22.17, 22.07; ESI-MS: m/z calcd for C39H69N3O26: 995.4067; found 1018.4106 (M + Na)+.
Figure imgf000152_0001
[00445] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-{2-O- acetyl3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)}-[2-O-acetyl-3,4,6-tri-O-benzyl-α-D- mannopyranosyl-(1→6)]-2,4-di-O-benzyl-α-D-mannopyranosyl-(1→6)}-2-O-acetyl-β-D- mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranosyl)(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S9e): A mixture of Silver triflate (0.127 g, 0.497 mmol), Bis(cyclopentadienyl) hafnium dichloride (0.121 g, 0.319 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at room temperature for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 4 (0.103 g, 0.085 mmol) and acceptor S9c (0.125 g, 0.071 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h, quenched with Et3N, diluted with CH2Cl2 and filtered through celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S9e (0.110 g, 52%) as colorless foam. TLC: (acetone: toluene = 2/8, v/v): Rf = 0.36; 1H NMR (600 MHz, CDCl3): δ 7.77-7.40 (m, 8H, Ar-H), 7.32-7.07 (m, 85H, Ar-H), 6.99-6.88 (m, 4H, Ar-H), 6.79-6.68 (m, 6H, Ar-H), 5.44 (s, 1H, H-2d), 5.43 (s, 1H, H-2e), 5.41 (s, 1H, H-2e'), 5.29 (d, J = 3.4 Hz, 1H, H-2c), 5.18 (s, 2H, H-1d,d'), 5.16 (s, 1H, H-1e), 5.09 (s, 1H, H-1e'), 4.92 (s, 1H, H-1c), 4.91 (d, J = 8.5 Hz, 1H, H-1a), 4.83- 4.78 (q, 1H), 4.84-4.73 (m, 6H), 4.65-4.61 (m, 2H), 4.60-4.57 (m, 5H), 4.524.35 (m, 17H), 4.27 (d, J = 12.3Hz, 1H), 4.20-4.19 (m, 1H), 4.10-3.99 (m, 6H), 3.97-3.70 (m, 13H), 3.69- 3.57 (m, 8H), 3.56-3.31 (m, 6H), 3.30 (dd, J = 3.2, 9.2 Hz, 1H), 3.30-3.18 (m, 5H), 2.97-2.96 (m, 1H), 2.89-2.79 (m, 2H, -CCH2C-, linker), 2.12 (s, 3H, -C(O)CH3), 2.07 (s, 3H, - C(O)CH3), 2.01 (s, 6H, -C(O)CH3), 1.33-1.23 (m, 4H, -CCH2C-, linker), 1.06-0.99 (m, 2H, - CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.56, 170.42, 170.26, 170.02, 168.45, 168.69, 138.95, 138.93, 138.72, 138.68, 138.58, 138.24, 138.22, 138.07, 133.83, 132.09, 131.76, 128.87, 128.79, 128.67, 128.63, 128.61, 128.58, 128.52, 128.42, 128.13, 128.06, 127.99, 127.92, 127.81, 127.76, 127.74, 127.46, 127.08, 123.71, 123.36, 100.13 (C-1e,e', 1 J C,H = 169.2 Hz), 99.39 (C-1b, 1 J C,H = 162.2 Hz), 98.35 (C-1d, 1 J C,H = 171.5 Hz), 98.31 (C-1a, 1 J C,H = 160.2 Hz), 97.16 (C-1d', 1 J C,H = 170.5 Hz), 76.20, 76.05, 75.42, 74.97, 74.89, 74.80, 74.70, 74.65, 74.47, 74.28, 73.94,73.68, 73.26, 72.60, 72.25, 72.20, 71.70, 71.50, 69.15, 69.07, 69.04, 68.99, 68.50, 68.45, 67.80, 65.54, 56.73, 55.90, 51.29,31.14, 29.91, 28.87, 28.47, 23.19, 21.33, 21.27, 21.19l; HRMS (MALDI-TOF): m/z calcd for C176H185N5O42: 3042.2400; found 3065.2210 (M + Na)+.
Figure imgf000154_0001
[00446] 5-Aminopentyl-α-D-mannopyranosyl(1→3),[di-(α-D-mannopyranosyl)-(1→3), (1→6)-α-D-mannopyranosyl](1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl -(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G4):- Heptasaccharide S9e (0.140 g, 0.024 mmoles), was deprotected by following the general procedure 2 (Method 1) to obtain title compound G4 (0.039 g, 29%) as a white solid. 1H NMR (600 MHz, D2O): δ 5.09 (s, 1H, H-1d), 4.89 (s, 1H, H-1d'), 4.86 (d, J = 1.5 Hz, 1H, H-1e), 4.75 (d, J = 1.5 Hz, 1H, H-1e'), 4.76 (s, 1H, overlapped with D2O, H-1c), 4.50 (d, J = 7.8 Hz, 1H, H-1a), 4.35 (d, J = 7.9 Hz, 1H, H-1b), 4.17 (d, J = 1.7 Hz, 1H), 4.07– 4.05 (m, 1H), 4.00-3.97 (m, 2H), 3.94- 3.37 (m, 40H), 2.90-2.85 (m, 2H, -CH2Nlinker), 1.98 (s, 3H, -C(O)CH3), 1.94 (s, 3H, - C(O)CH3), 1.61-1.46 (m, 4H, -CCH2C-, linker), 1.35-1.26 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 177.2, 172.3, 102.44, 101.44, 101.01, 100.37, 99.85, 99.25, 80.54, 79.49, 79.28, 78.58, 74.45, 74.43,72.50, 71.93, 70.64, 70.24, 70.15, 70.04, 70.01, 69.87, 69.46, 69.39, 66.69, 66.66, 65.94,65.91, 65.56, 65.13, 65.12, 60.93, 60.91, 60.43, 60.13, 60.04, 59.97, 54.90, 54.86, 39.28,27.98, 26.48, 22.08, 22.02, 21.99; ESI-MS: m/z calcd for C51H89N3O36: 1319.5123; found 1342.5165 (M + Na)+.
Figure imgf000155_0001
[00447] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6- tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2- O-acetyl-4,6-O-benzylidene-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2- phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranoside (S10a): A mixture of Silver triflate (0.328 g, 1.28 mmol),
Bis(cyclopentadienyl) hafnium dichloride (0.340 g, 0.897 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to 40 °C, a solution of donor 2 (0.383 g, 0.282 mmol) and acceptor 14 (0.350 g, 0.256 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h, quenched with Et3N, diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S10a (0.405 g, 58%) as colorless foam. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.46; 1H NMR (600 MHz, CDCl3): δ 7.89-7.35 (m, 8H, Ar-H), 7.38-7.12 (m, 56H, Ar-H), 7.12-7.08 (m, 3H, Ar-H), 7.03-6.88 (m, 7H, Ar-H), 6.78-6.69 (m, 4H, Ar-H), 5.50 (s, 1H, H-1f), 5.37 (d, J = 1.4 Hz, 1H, H-2c), 5.25 (s, 1H, Ph-CH-, benzylidene), 5.23-5.17 (m, 3H, overlapped, H-1d,e,f), 4.98 (s, 1H, H-1c), 4.95 (d, J = 7.5 Hz, 1H, H-1a), 4.91-4.53 (m, 5H), 4.69-4.58 (m, 3H), 4.554.28 (m, 16H), 4.25-4.00 (m, 13H), 3.95-3.91 (m, 1H), 3.91-3.60 (m, 14H), 3.58 (d, J = 12 Hz, 1H), 3.51-3.45 (m, 4H), 3.42-3.38 (m, 3H), 3.29-3.10 (m, 3H), 2.98-2.78 (m, 3H), 2.08 (s, 3H, -C(O)CH3), 1.99 (s, 3H, -C(O)CH3), 1.35-1.23 (m, 4H, -CCH2C-, linker), 1.07-1.00 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.38, 169.81, 168.76, 168.26, 139.06, 138.95, 138.92, 138.87, 138.60, 137.36, 128.85, 128.66, 128.64, 128.58, 128.55, 128.48, 128.43, 128.39, 128.35, 128.26, 128.10, 128.02, 127.82, 127.71, 101.48, 100.08, 99.75, 99.39, 98.36, 97.27, 77.80, 78.75, 76.10, 75.38, 74.93, 74.82, 74.70, 73.58, 73.28, 73.21, 73.06, 72.79, 72.65, 72.57, 72.17, 71.01, 69.60, 69.10, 68.96, 68.63, 66.74, 56.85, 55.97, 51.37, 28.95, 28.54, 23.27, 21.43, 21.09; ESI-MS: m/z calcd for C159H163N5O35: 2703.1054; found 2726.1214 (M + Na)+.
Figure imgf000156_0001
[00448] 5-Aminopentyl-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D- manno-pyranosyl-(1→3)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G5): Hexasaccharide S10a (0.140 g, 0.051 mmoles), was deprotected by following general procedure 2 (Method 1) to obtain the title compound G5 (0.025 g, 42%) as white solid. 1H NMR (600 MHz, D2O): δ 5.32 (s, 1H, H-1d), 5.27 (s, 1H, H-1e), 5.01 (s, 1H, H-1f), 4.74 (s, 1H, H-1c), 4.56 (d, J = 7.8 Hz, 1H, H-1a), 4.63 (d, J = 7.8 Hz, 1H, H-1b),4.18 (d, J = 3.3 Hz, 1H), 4.07 (s, 1H), 4.04 (d, J = 3.2 Hz, 1H), 4.03 (d, J = 3.1 Hz, 1H), 3.32-3.33 (m, 35H), 2.05 (t, J = 11.2 Hz, 2H, - CH2NH2, linker), 2.03 (s, 3H, -C(O)CH3), 2.00 (s, 3H, -C(O)CH3), 1.64 (m, 2H, -CCH2C-, linker), 1.50 (m, 2H, -CCH2C-, linker), 1.36 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.54, 174.38, 102.17 (C-1e, 1 J C,H = 170.2 Hz), 101.34 (C-1b, 1 J C,H = 161.2 Hz), 101.014 (C-1d, 1 J C,H = 169.8 Hz), 100.70 (C-1f, 1 J C,H = 172.2 Hz), 100.56 (C-1a, 1 J C,H = 160.2 Hz), 99.85, 80.50, 79.25, 78.66, 78.55, 78.47, 76.12, 74.48, 73.37, 73.13, 72.33, 71.88, 70.24, 70.17, 70.05, 69.95, 69.89, 66.95, 66.81,66.71, 65.81, 61.01, 60.97, 60.88, 60.76, 60.02, 59.92, 54.92, 39.25, 27.99, 26.32, 23.19, 22.06, 22.04; ESI-MS: m/z calcd for C45H79N3O31: 1157.4590; found 1180.4591 (M + Na)+.
Figure imgf000157_0001
[00449] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6- tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2- O-acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S10b):- To a solution of S10a (0.205 g, 0.075 mmol) in 10 mL acetonitrile was added p- toluene sulfonic acid monohydrate (0.020 g, 0.113 mmol), stirred at room temperature for 9 h. The reaction was quenched with Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 20% EA in toluene) to give diol S10b (0.120 g, 60%). TLC: (acetone: toluene = 2/8, v/v): Rf = 0.26; 1H NMR (600 MHz, CDCl3): δ 7.83-7.62 (m, 8H, Ar-H), 7.41-7.06 (m, 57H, Ar-H), 6.95-6.89 (m, 6H, Ar-H), 6.73-6.71 (m, 2H, Ar-H), 5.50 (d, J = 4.8 Hz, 1H, H-2f), 5.23 (d, J = 1.8 Hz, 1H, H-1d), 5.22 (d, J = 3.8 Hz, 1H, H-1c), 5.19 (d, J = 3.2 Hz, 1H, H-1e), 5.18 (s, 1H, H-1f), 5.03 (d, J = 7.8 Hz, 1H, H-1a), 4.88 (t, J = 7.8 Hz, 1H), 4.82-4.74 (m, 5H), 4.68-4.38 (m, 21H), 4.33 (d, J = 7.8 Hz, 1H), 4.29 (d, J = 7.9 Hz, 1H), 4.20-4.00 (m, 8H), 3.95-3.71 (m, 9H), 3.69-3.53 (m, 6H), 3.52-3.33 (m, 8H), 3.29-3.15 (m, 5H), 2.90-2.79 (m, 2H), 2.08 (s, 3H, -C(O)CH3), 1.92 (s, 3H, -C(O)CH3), 1.35-1.20 (m, 4H, -CCH2C-, linker), 1.081.01 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.40, 169.88, 168.68, 138.20, 138.94, 138.78, 138.71, 138.56, 138.48, 138.38, 138.21, 138.02, 134.30, 133.84, 132.02, 128.78, 128.65, 128.63, 128.43, 128.40, 128.38, 128.25, 128.15, 128.06, 127.94, 127.88, 127.84, 127.77, 127.69, 127.65, 127.56, 127.10, 123.90, 123.41, 100.98, 99.83, 98.34, 97.32, 78.31, 78.17, 78.11, 78.00, 76.22, 75.52, 75.28, 75.05, 74.82, 74.40, 73.98, 73.67, 73.58, 73.36, 73.06, 72.59, 72.48, 72.42, 72.09, 71.32, 70.52, 69.46, 69.09, 68.83, 68.72, 68.42, 68.20, 67..61, 62.57, 56.77, 55.98, 51.37, 29.99, 29.65, 28.94, 28.54, 23.27, 21.44, 21.13, 14.41; ESI-MS: m/z calcd for C152H159N5O35: 1615.0741; found 2638.0754 (M + Na)+.
Figure imgf000159_0001
[00450] 5-Azidopentyl-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6- tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)- {2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O-benzyl-α-D-manno- pyranosyl-(1→3)-[2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→2)-3,4,6-tri-O- benzyl-α-D-mannopyranosyl-(1→6)]-2,4-di-O-benzyl-α-D-mannopyranosyl-(1→6)}-2-O- acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D -glucopyranoside (S10c): A mixture of hexasaccharide acceptor S10a (0.1 g, 0.038 mmol), thiomannoside donor 5 (0.104 g, 0.045 mmol) and activated 4 Å molecular sieves (0.5 g) in CH3CN (10 mL) was stirred at rt for 1 h. The resulting mixture was cooled to -10 °C, tris(4-bromophenyl)aminium hexachloroantimonate (0.096 g, 0.114 mmol) was added and stirred at rte for 6 h. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, reaction was quenched by Et3N. The reaction mixture was diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S10c (0.095 g, 52%) as colorless foam. TLC: (acetone: toluene = 2/8, v/v): Rf = 0.41; 1H NMR (600 MHz, CDCl3): δ 7.77-7.50 (m, 8H, Ar-H), 7.29-6.98 (m, 126H, Ar-H), 6.95-6.89 (m, 4H, Ar-H), 6.746.64 (m, 5H, Ar-H), 5.56 (s, 1H, H-2f), 5.53 (s, 1H, H-2h), 5.51 (s, 1Hh'), 5.34 (s, 1H, H-2c), 5.32 (d, J = 12.2 Hz, 2H), 5.18 (d, J = 7.8 Hz, 1H), 5.12 (s, 1H), 5.08 (s, 1H), 5.04 (s, 2H), 4.59-3.75 (m, 116H), 3.26-3.16 (m, 4H), 3.08-3.02 (m, 2H), 2.93-2.83 (m, 2H), 2.12 (s, 3H), 2.06 (s, 3H), 2.06 (s, 3H), 1.97 (s, 3H), 1.39-1.26 (m, 4H), 1.07-1.05 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 170.12, 170.03, 169.76, 168.14, 167.36, 138.64, 138.54, 138.45, 138.41, 138.27, 138.07, 133.68, 133.57, 131.74, 129.05, 128.62, 128.57, 128.51, 128.33, 128.23, 128.14, 128.06, 127.99, 127.94, 127.81, 127.78, 127.73, 127.45, 101.24, 99.81, 99.59, 99.48, 99.34, 99.24, 99.05, 98.02, 96.95, 79.82, 79.23, 78.33, 78.24, 78.14, 75.86, 75.22, 75.12, 75.02, 74.93, 74.77, 74.57, 74.47, 74.38, 74.30, 74.17, 73.29, 73.11, 72.50, 72.20, 71.94, 71.35, 71.25, 69.13, 69.03, 68.79, 68.53, 68.48, 68.35, 68.17, 67.40, 56.56, 55.69, 51.09, 28.66, 28.26, 22.99, 21.17, 21.12; HRMS (MALDI-TOF): m/z calcd for C284H297N5O62: 4772.0232; found 4794.9783 (M + Na)+.
Figure imgf000161_0001
[00451] 5-Aminopentyl-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D- manno-pyranosyl-(1→3)-{α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-[α-D- manno-pyranosyl-(1→2)-α-D-mannopyranosyl-(1→6)]-α-D-mannopyranosyl-(1→6)}-β-D- manno-pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2- deoxy-β-D-glucopyranoside (G6): Compound S10c (0.120 g, 0.024 mmoles) was deprotected by following general procedure 2 (Method 1) to get Man9GlcNAc2 G6 (0.012 g, 26%) as a white solid. 1H NMR (600 MHz, D2O): δ 5.40 (s, 1H, H-1d), 5.33 (s, 1H, H-1d'), 5.30 (s, 1H, H-1e), 5.14 (s, 1H, H-1), 5.05 (s, 1H, H-1), 5.03 (d, J =2.4 Hz, 2H, H-1), 4.86 (s, 1H, H- 1), 4.58 (d, J = 7.8 Hz, 1H, H-1a), 4.48 (d, J = 7.8 Hz, 1H, H-1b), 4.22 (d, J = 2.4 Hz, 1H), 4.14 (s, 1H), 4.143.95 (m, 12H), 3.94-3.59 (m, 54H), 3.50-3.48 (m, 1H), 3.02 (t, J = 9.2 Hz, 2H), 2.06 (s, 3H, -C(O)CH3), 2.02 (s, 3H, -C(O)CH3), 1.68-1.63 (m, 2H, -CCH2C-, linker), 1.59-1.56 (m, 2H, -CCH2C-, linker), 1.41-1.37 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.47, 171.01, 102.24 (C-1d, 1 J C,H = 171.8 Hz), 102.21 (C-1d', 1 J C,H = 169.0 Hz), 102.19 (C-1e, 1 J C,H = 173.8 Hz), 101.43, 101.03, 100.82, 100.59 (C-1a, 1 J C,H = 162.8 Hz), 100.21, 99.61, 97.97 (C-1b, 1 J C,H = 159.8 Hz), 81.86, 79.32, 78.88, 78.63, 78.45, 74.50, 74.48, 74.14, 73.39, 73.27, 73.20, 73.17, 72.69, 72.36, 71.90, 71.61, 70.21, 70.03, 69.93, 69.37, 67.01, 66.94, 66.90, 66.85, 66.81, 66.76, 65.42, 65.40, 65.07, 64.90, 61.11, 61.06, 61.01, 60.91, 60.06, 59.94, 54.95, 39.29, 38.61, 28.02, 26.34, 22.16, 22.10, 22.06; ESI-MS: m/z calcd for C75H129N3O56: 1967.7231; found 1990.7279 (M + Na)+.
[00452 S nthesis of h brid t e oli osaccharides G7-G14 S
Figure imgf000162_0001
Figure S2 | Structures of hybrid type glycans and their fragments [00453] Synthesis of hybrid type sugars commenced with condensation of 14 with 6 catalyzed by AgOTf/Cp2HfCl2 to give pentasaccharide S11a in 63% yield (Scheme S11). Reductive benzilidine opening resulted in diol S11b, which was further glycosylated at 6”-O with trimannosyl thioglycoside 3 to afford S11c in 55% yield. Cp2HfCl2 /AgOTf mediated condensation of acceptor S11b with 6 resulted in the formation of S11d in 58% yield.
Figure imgf000163_0001
[00454] Scheme S11 | Preparation of octasaccharide G7 and heptasaccharide G8. a, 6, AgOTf, Cp2HfCl2, Toluene, 4 Å MS, -40 °C, 4 h, 63%; b, pTsOH, CH3CN, 5 h, 78%; c, 3, (BrC6H4)3NSbCl6, CH3CN, 4 Å MS, -10 °C to RT, 4 h, 55%; d, 6, AgOTf, Cp2HfCl2, Toluene, 4 Å MS, -40 °C, 4 h, 58%; e, (1) NH2CH2CH2NH2, nBuOH, 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2; G7:26; G8:32%.
Figure imgf000163_0002
[00455] 5-Azidopentyl-O-2-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl-(1→2)-O-(3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O-acetyl-4,6-O- benzylidine-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S11a): A mixture of trichloroacetimidate donor 6 (0.341 g, 0.308 mmol), chitobiose acceptor 14 (0.350 g, 0.256 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at rt for 1 h. The reaction was cooled to -40 °C, boron trifluoride ethyl etherate (14.8 µL, 0.129 mmol) was then added slowly and the resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0% → 10% EA in toluene) to afford S11a (0.360 g, 63%) as white foam. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.56; 1H NMR (600 MHz, CDCl3): δ 7.84-7.55 (m, 12H, Ar-H), 7.45-7.10 (m, 28H, Ar-H), 7.06-6.90 (m, 18H, Ar-H), 6.75-6.71 (m, 4H, Ar-H), 5.37 (d, J = 8.4 Hz, 1H, H-1), 5.21 (d, J = 8.4 Hz, 1H, H-1), 5.19 (s, 1H, Ph-CH, benzylidene), 5.09 (t, J = 9.0 Hz, 1H), 4.93-4.76 (m, 6H), 4.57 (s, 1H), 4.54 (d, J = 12.0 Hz, 1H), 4.45-4.07 (m, 20H), 3.69-3.15 (m, 22H), 3.02-3.00 (m, 1H), 2.86-2.81 (m, 2H, linker), 2.25 (s, 3H, -C(O)CH3), 1.84 (s, 3H, -C(O)CH3), 1.35-1.23 (m, 4H, -CCH2C-, linker), 1.07-1.02 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.68, 170.05, 167.88, 138.98, 138.89, 138.85, 138.71, 138.63, 138.14, 138.07, 137.78, 134.08, 133.90, 133.46, 132.06, 131.81, 129.32, 128.90, 128.83, 128.67, 128.55, 128.50, 128.34, 128.27, 127.95, 127.79, 127.70, 127.60, 101.00, 99.41, 98.38, 97.91, 97.29, 80.38, 79.02, 76.82, 76.76, 76.52, 76.14, 75.25, 74.90, 74.83, 74.67, 74.51, 74.44, 73.68, 73.52, 73.38, 73.06, 73.02, 72.93, 71.46, 70.65, 70.40, 70.03, 69.66, 69.14, 68.52, 67.56, 56.83, 55.98, 55.85, 51.37, 29.99, 28.95, 28.55, 23.28, 21.67, 21.19; ESI-MS: m/z calcd for C133H132N6O31: 2309.8862; found 2332.8861 (M + Na)+.
Figure imgf000165_0001
[00456] 5-Azidopentyl-O-2-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl(1→2)-O-(3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O-acetyl-β-D- mannopyranosyl -(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl)- (1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S11b): p-Toluene sulfonic acid monohydrate (0.020 g, 0.143 mmol) was added to a solution of S11a (0.220 g, 0.095 mmol) in acetonitrile (20 mL) and the resulting reaction mixture was stirred at rt for 5h. The reaction was quenched by adding Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to give diol S11b (0.165 g, 78%). TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.32; 1H NMR (600 MHz, CDCl3): δ 7.89-7.43 (m, 12H, Ar-H), 7.35-7.16 (m, 28H, Ar-H), 7.09-7.05 (m, 5H, Ar-H), 7.03-6.89 (m, 9H, Ar-H), 6.75-6.72 (m, 3H, Ar-H), 5.30 (d, J = 8.4 Hz, 1H, H-1a), 5.23 (d, J = 8.4 Hz, 1H, H-1b), 5.12 (d, J = 9.0 Hz, 1H), 5.09 (t, J = 9.8 Hz, 1H), 4.95 (d, J = 12.0 Hz, 1H), 4.90 (d, J = 8.4 Hz, 1H, H-1e), 4.87-4.80 (m, 2H), 4.58-4.55 (m, 2H), 4.50-4.41 (m, 10H, overlapped, H-1d), 4.37-4.34 (m, 3H), 4.27-4.24 (m, 2H), 4.18-4.15 (m, 2H), 4.10-3.92 (m, 5H), 3.73-3.70 (m, 2H), 3.65-3.61 (m, 2H), 3.59-3.51 (m, 5H), 3.47-3.38 (m, 6H), 3.23- 3.17 (m, 4H), 3.04 (dd, J = 3.6, 9.0 Hz, 1H), 3.01-3.98 (m, 1H), 2.83-2.78 (m, 3H), 2.38 (s, 3H, -C(O)CH3), 1.90 (s, 3H, -C(O)CH3), 1.36-1.22 (m, 4H, -CCH2C-, linker), 1.06-1.01 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.93, 170.05, 168.77, 167.86, 167.69, 138.90, 138.83, 138.65, 138.47, 138.23, 138.14, 138.07, 138.04, 134.35, 134.13, 133.91, 132.04, 131.84, 131.72, 128.81, 128.65, 128.64, 128.62, 128.54, 128.53, 128.48, 128.46, 128.36, 128.17, 128.09, 128.02, 127.99, 127.97, 127.92, 127.91, 127.83, 127.77, 127.74, 127.63, 127.13, 124.73, 123.97, 123.43, 123.08, 118.73, 100.25 (C-1e), 98.37 (C-1d), 98.21 (C-1c), 97.86 (C-1b), 97.30 (C-1a), 82.86, 80.05, 78.38, 76.92, 76.15, 75.72, 75.60, 75.45, 74.86, 74.83, 74.70, 74.42, 74.24, 73.75, 73.42, 73.38, 72.82, 70.81, 70.60, 70.27, 69.99, 69.50, 69.15, 69.13, 68.53, 67.88, 66.28, 62.98, 56.78, 55.99, 55.88, 51.37, 32.21, 29.98, 28.94, 28.54, 23.27, 21.69, 21.18; ESI-MS: m/z calcd for C126H128N6O31:
2221.8549; found 2244.8529 (M +Na)+ .
Figure imgf000166_0001
[00457] 5-Azidopentyl-O-{4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl-(1→2)}-O-{3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-{2-O-acetyl-3,4,6-tri- O-benzyl-α-D-mannopyranosyl-(1→3)}-[2-O-acetyl-3,4,6-tri-O-benzyl-α-D-manno- pyranosyl(1→6)]-2,4-di-O-benzyl-α-D-mannopyranosyl-(1→6)}-2-O-acetyl-β-D-manno- pyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl)-(1→4)- O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S11c): A mixture of pentasaccharide acceptor S11b (0.150 g, 0.067 mmol), thiomannoside donor 3 (0.110 g, 0.080 mmol) and activated 4 Å molecular sieves (0.500 g) in CH3CN (10 mL) was stirred at rt for 1 h. The resulting mixture was cooled to -10 °C, tris (4-bromophenyl) aminium hexachloroantimonate (0.170 g, 0.201 mmol) was added and resulting reaction was stirred at room temperature for 4 h. TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched by Et3N. The reaction mixture was diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S11c (0.130 g, 55%) as colorless foam. TLC: (ethyl acetate: toluene= 1/9, v/v): Rf = 0.42; 1H NMR (600 MHz, CDCl3): δ 7.71-7.30 (m, 8H, Ar-H), 7.28-7.10 (m, 70H, Ar-H), 7.97-6.86 (m, 12H, Ar-H), 6.69 (m, 7H, Ar-H), 5.47 (d, J = 8.4 Hz, 2H), 5.44 (s, 1H), 5.32 (d, J = 8.4 Hz, 1H, H-1a), 5.15 (d, J = 8.4 Hz, 1H, H-1b), 5.13-5.10 (m, 2H), 5.00 (s, 1H, H-1d), 4.95 (s, 1H, H-1f), 4.91 (s, 2H, H-1g, H-1g’), 4.87-4.73 (m, 8H), 4.62 (d, J = 8.7 Hz, 1H), 4.57-4.28 (m, 26H), 4.15-3.70 (m, 20H), 3.68- 3.40 (m, 15H), 3.38-3.25 (m, 6H), 3.24-3.09 (m, 5H), 2.98 (dd, J = 2.3, 7.8Hz, 1H), 2.89-2.79 (m, 2H), 2.73-2.71 (m, 1H), 2.27 (s, 3H, -C(O)CH3), 2.05 (s, 3H, -C(O)CH3), 1.99 (s, 3H, - C(O)CH3), 1.88 (s, 3H, -C(O)CH3), 1.32-1.28 (m, 4H, -CCH2C-, linker), 1.07-0.98 (m, 2H, - CCH2C-, linker); 13C NMR (150 MHz, CDCl3): δ 170.26, 168.89, 138.38, 128.47, 128.37, 128.32, 128.30, 128.26, 128.24, 128.19, 128.08, 128.04, 127.91, 127.86, 127.73, 127.56, 127.49, 127.39, 127.26, 100.35, 100.23, 99.89, 99.56, 99.23, 98.54, 98.33, 98.23, 78.43, 76.09, 75.37, 75.07, 74.08, 74.44, 74.04, 73.47, 73.31, 72.63, 68.81, 51.08, 29.71, 29.37, 28.66, 28.25, 22.98; HRMS (MALDI-TOF): m/z calcd for C204H210N6O48; 3513.4134 found 3536.4050 (M +Na)+.
Figure imgf000168_0001
[00458] 5-Aminopentyl-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D- mannopyranosyl-(1→3),[di-(α-D-mannopyranosyl)-(1→3),(1→6)-α-D- mannopyranosyl](1→6)-β-D-manno-pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G7): Compound S11c (0.105 g, 0.030 mmole) was deprotected by following general procedure 2 (Method 1) to get the title compound G7 (0.012 g, 26%) as a white solid. 1H NMR (600 MHz, D2O): δ 5.09 (d, J = 1.2 Hz, 1H, H-1d), 5.02 (d, J = 8.4 Hz, 1H, H-1a), 4.95 (s, 1H, H-1f), 4.91 (s, 1H, H- 1g), 4.85 (s, 1H, H-1g'), 4.78 (S, 1H, H-1c), 4.61 (d, J = 7.8 Hz, 1H, H-1e), 4.51 (d, J = 7.8 Hz, 1H, H-1b), 4.22 (t, J = 10.2 Hz, 2H), 4.18 (dd, J = 1.8, 3.0 Hz, 1H), 4.00 (dd, J = 1.8, 3.1 Hz, 1H), 4.08-3.38 (m, 47H), 3.03 (t, J = 8.2 Hz, 2H, -NCH2-, linker), 2.09 (s, 3H, - C(O)CH3), 2.08 (s, 3H, -C(O)CH3), 2.01 (s, 3H, -C(O)CH3), 1.71-1.66 (m, 2H, -CCH2C-, linker), 1.62-1.59 (m, 2H, -CCH2C-, linker), 1.44-1.40 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.91, 174.42, 171.02, 110.64 (C-1d, 1 J C,H =174 Hz ), 102.32, 101.48, 100.51 (C-1a, 1 J C,H = 161 Hz ), 100.44, 100.15, 99.26, 97.58 (C-1g, 1 J C,H =169.6 Hz), 79.48, 78.86, 78.72, 76.64, 76.04, 75.72, 74.65, 74.51, 74.42, 73.31, 72.69, 72.35, 72.09, 71.96, 70.86, 70.57, 70.34, 70.12, 70.09, 69.94, 69.42, 67.39, 66.70, 66.36, 65.54, 65.14, 61.68, 61.02, 60.93, 39.31, 38.62, 28,03, 26.39, 22.58, 22.20, 22.11, 22.08, 21.82; ESI-MS: m/z calcd for C59H102N4O41; 1522.6092 found 1523.6148 (M +H)+.
Figure imgf000169_0001
[00459] 5-Azidopentyl-O-di-[{4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- gluco-pyranosy-(1→2)}-O-{3,4,6-tri-O-benzyl-α-D-mannopyranosyl}]-(1→3),(1→6)-2-O- acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S11d):- A mixture of Silver triflate (0.080 g, 0.315 mmol), Bis(cyclopentadienyl)hafnium dichloride (0.084 g, 0.220 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 6 (0.091 g, 0.094 mmol) and acceptor S11b (0.140 g, 0.063 mmol) in 5 mL toluene was added. The mixture was stirred for 4 h, quenched with Et3N, diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S11d (0.110 g, 58%) as colorless foam. TLC: (acetone: toluene =2/8, v/v): Rf = 0.39; 1H NMR (600 MHz, CDCl3): δ 7.62-7.32 (m, 16H, Ar-H), 7.27-6.87 (m, 41H, Ar- H), 6.85-6.59 (m, 29H, Ar-H), 5.27 (d, J = 8.4 Hz, 1H), 5.16 (s, 1H), 5.14 (d, J = 3.6 Hz, 1H), 5.10 (d, J = 1.8 Hz, 1H), 4.98 (d, J = 3.6 Hz, 1H), 4.89-4.68 (m, 10H), 4.59-4.21 (m, 21H), 4.19-3.87 (m, 7H), 3.80 (dd, J = 3.2, 1.8 Hz, 1H), 3.70-3.52 (m, 7H), 3.51-3.28 (m, 8H), 3.27- 3.18 (m, 5H), 3.15-3.03 (m, 3H), 3.01 (dd, J = 3.2, 1.8 Hz, 1H), 2.912.75 (m, 5H), 2.73-2.69 (m, 1H), 2.27 (s, 3H), 1.98 (s, 3H), 1.86 (s, 3H), 1.32-1.23 (m, 4H), 1.03-0.99 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.09, 171.04, 170094, 167.91, 167.57, 139.19, 138.86, 138.63, 138.54, 138.42, 138.31, 138.21, 138.14, 137.93, 133.84, 133.71, 132.04, 131.80, 131.69, 128.80, 128.64, 128.39, 128.32, 128.13, 128.08, 127.79, 127.70, 127.60, 100.18, 100.00, 98.36, 97.88, 97.61, 97.30, 97.22, 80.14, 79.97, 79.31, 75.85, 75.56, 75.39, 75.30, 75.04, 74.71, 74.59, 73.95, 73.64, 73.24, 72.86, 72.14, 71.55, 71.37, 71.04, 70.53, 70.40, 70.15, 69.71, 69.12, 68.12, 65.40, 63.29, 56.34, 55.92, 51.45, 51.37, 51.27, 28.95, 28.54, 23.26, 21.13, 21.02; HRMS (MALDI-TOF): m/z calcd for C183H183N7O43; 3168.2306 found 3191.2375 (M +Na)+.
Figure imgf000170_0001
[00460] 5-Aminopentyl-di-[2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D- mannopyranosyl]-(1→3),(1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G8): Compound S11d (0.130 g, 0.041 mmol) was deprotected by following general procedure 2 (Method 1) to get the desired heptasaccharide G8 (0.015 g, 29%) as a white solid. 1H NMR (600 MHz, D2O): δ 5.99 (d, J = 8.5Hz, 1H, H-1a), 4.93 (s, 1H, H-1d), 4.83 (s, 1H, H-1d'), 4.76 (s, 1H, H-1c), 4.60 (d, J = 7.8 Hz, 1H, H-1b), 4.56 (d, J = 7.9 Hz, 1H, H-1e), 4.49 (d, J = 7.9 Hz, 1H, H-1e'), 4.27 (s, 2H), 4.11 (d, J = 1.8 Hz, 1H), 3.96-3.41 (m, 41H), 2.98 (t, J = 8.9 Hz, 2H, -NCH2-, linker), 2.13 (s, 3H, C(O)CH3), 2.09 (s, 3H, -C(O)CH3), 2.06 (s, 3H, -C(O)CH3), 2.01 (s, 3H, -C(O)CH3), 1.69-1.64 (m, 2H, -CCH2C-, linker), 1.60-1.57 (m, 2H, -CCH2C-, linker), 1.42-1.38 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.88, 174.78, 174.65, 174.42, 171.0, 101.39, 101.05, 100.61 (C-1c), 100.39 (C-1a), 99.55 (C-1e'), 97.60 (C-1d'), 97.20 (C-1d), 79.41, 79.28, 78.92, 76.63, 76.25, 75.79, 74.50, 73.64, 72.84, 71.95, 70.09, 69.89, 69.48, 67.39, 67.35, 66.20, 65.39, 61.66, 61.61, 60.75, 60.61, 59.96, 55.68, 54.98, 54.94, 39.30, 28.04, 26.35, 22.55, 22.31, 22.21, 22.12, 22.08; ESI-MS: m/z calcd for C55H95N5O36; 1402.5830; found 1403.5862 (M + H)+.
[00461] Preparation of glycans G12-G14
[00462] Stereoselective installation of trisaccharide antenna 7 at the 3-O position of the core trisaccharide acceptor 14 was performed under the promotion of Cp2HfCl2/AgOTf to afford hexasaccharide S12a. The p-toluene sulfonic acid-mediated reductive ring opening of S12a provided diol S12b. Considering the higher reactivity of the primary hydroxyl, S12b was further glycosylated at the 6-O position with trimannosyl thioglycoside 3 and, then, activated by the stable radical cation tris(4-bromophenyl) ammoniumyl hexachloroantimonate in a one electron transfer reaction to afford nonasaccharide S12c. With compound S12c in hand, a series of functional group transformations were carried out to afford the desired fully deprotected glycan G12. The precursor oligosaccharide G12, is an appropriate starting material for sialylation by α-2,6 or 2,3 sialyltransferase derived from marine bacteria, known for their broader acceptor specificity and no intrinsic sialidase activity. Sialyl transferase (SiaT)-mediated enzymatic terminal sialylation1-4 of G12 efficiently permitted access to α- 2,6 and α-2,3 sialylated glycans G13 and G14, respectively (Scheme S12).
Figure imgf000172_0001
[00463] Scheme S12 | Preparation of G12-G14. i) 7, Cp2HfCl2, AgOTf, 4 Å MS, -40 °C, 2 h, 63%; ii) p-TsOH, CH3CN, 5 h, 78%; iii) 3, (BrC6H4)3NSbCl6, CH3CN, 4 Å MS, -10 °C to RT, 4 h, 55%; iv) (1) NH2CH2CH2NH2, n-BuOH, 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O : HCOOH (5:3:2), H2; 62%; v) CMP-β-D-Sialic acid, α-2,6- or 2,3-sialyltransferase, G13: 60%; G14: 56%;
Cp2HfCl2: Bis(cyclopentadienyl) hafnium dichloride; AgOTf: Silver
trifluromethanesulfonate; (BrC6H4)3NSbCl6: Tris (4-bromophenyl) ammoniumyl hexachloroantimonate.
Figure imgf000173_0001
[00464] 5-Azidopentyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6- O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)-O-(3,4,6-tri-O-benzyl-α-D- mannopyranosyl-(1→3)-2-O-acetyl-4,6-O-benzylidine-β-D-mannopyranosyl-(1→4)-O-(3,6- di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2- deoxy-2-phthalimido-β-D-glucopyranoside (S12a): A mixture of silver triflate (0.327 g, 1.28 mmol), bis (cyclopentadienyl) hafnium dichloride (0.339 g, 0.896 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 7 (0.430 g, 0.307 mmol) and acceptor chitobiose trisaccharide 14 (0.35 g, 0.256 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford S12a (0.500 g, 71%) as white foam. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.62; 1H NMR (600 MHz, CDCl3): δ 7.85-7.49 (m, 8H, Ar-H), 7.02-7.39 (m, 44H, Ar-H), 7.19-7.02 (m, 11H, Ar-H), 6.99-6.90 (m, 6H, Ar-H), 6.83-6.78 (m, 3H, Ar-H), 6.75-6.70 (m, 5H, Ar-H), 5.310 (t, J = 7.5 Hz, 1H, H- 2f), 5.27 (d, J = 8.1 Hz, 1H, H-1a), 5.25 (d, J = 8.4 Hz, 1H, H-1e), 5.15 (d, J = 2.3 Hz, 1H), 5.01 (s, 1H, Ph-CH, benzylidene), 4.90-4.80 (m, 7H), 4.62 (d, J = 8.5Hz, 1H), 4.58-4.53 (m, 3H), 4.52-4.38 (m, 10H), 4.32-4.13 (m, 11H), 4.12-4.05 (m, 5H), 4.02 (m, 1H), 3.89 (d, J = 3.2 Hz, 1H), 3.75-3.73 (m, 2H), 3.72-3.49 (m, 8H), 3.48-3.37 (m, 5H), 3.34-3.29 (m, 4H), 3.29-3.18 (m, 4H), 2.98 (m, 1H), 2.89-2.79 (m, 2H, linker), 2.29 (s, 3H, -C(O)CH3), 1.99 (s, 3H, -C(O)CH3), 1.49-1.30 (m, 4H, -CCH2C-), 1.10-1.00 (m, 2H, -CCH2C-); 13C NMR (150 MHz, CDCl3): δ 170.8, 169.4, 168.7, 167.7, 139.1, 139.9, 138.9, 138.8, 138.8, 138.5, 138.2, 138.2, 138.1, 137.9, 137.6, 134.2, 133.8, 133.1, 131.9, 131.8, 131.6, 129.1, 128.8, 128.6, 128.5, 128.4, 128.4, 128.4, 128.3, 128.3, 128.2, 128.1, 128.0, 128.0, 127.9, 127.8, 127.8, 127.7, 127.7, 127.5, 127.5, 127.4, 127.3, 127.0, 126.7, 126.1, 123.8, 123.3, 122.8, 100.88, 100.83, 99.94, 99.38, 98.43, 98.30, 97.26, 80.31, 79.00, 78.05, 77.61, 76.42, 76.31, 76.1,. 75.1, 74.8, 74.7, 74.6, 74.6, 74.4, 74.4, 74.2, 73.6, 73.4, 73.3, 72.9, 72.8, 72.2, 71.8, 71.7, 70.4, 70.0, 69.8, 69.0, 68.8, 68.4, 68.2, 67.7, 67.6, 56.756.0, 55.9, 51.3, 28.8, 28.4, 23.2, 21.7, 21.2; ESI-MS: m/z calcd for C160H160N6O36; 2742.0799 found 2765.0952 (M +Na)+.
Figure imgf000174_0001
[00465] 5-Azidopentyl-O-2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)-O-3,6- O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)-O-(3,4,6-tri-O-benzyl-α-D- mannopyranosyl-(1→3)-2-O-acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2- deoxy-2-phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2- phthalimido-β-D-glucopyranoside (S12b): To a solution of S12a (0.601 g, 0.219 mmol) in acetonitrile (10 mL) was added p-toluene sulfonic acid monohydrate (0.046 g, 0.328 mmol), stirred at rt for 2 h. The reaction was quenched with Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to afford diol S12b (0.460 g, 78%). TLC: (acetone: toluene = 2/8, v/v): Rf = 0.32; 1H NMR (600 MHz, CDCl3): δ 7.91-7.42 (m, 12H, Ar-H), 7.39-7.12 (m, 41H, Ar-H), 7.10-6.93 (m, 13H, Ar-H), 6.85-6.81 (m, 3H, Ar-H), 6.78-6.73 (m, 3H, Ar-H), 5.33 (t, J = 7.8 Hz, 1H, H-2f), 5.23 (t, J = 8.4 Hz, 2H, H-1), 5.08 (d, J = 6.2 Hz, 1H), 4.97 (d, J = 8.9 Hz, 1H, H-1), 4.94-4.80 (m, 5H), 4.64-4.60 (m, 2H), 4.49-4.21 (m, 21H), 4.19-4.15 (m, 2H), 4.15-3.89 (m, 8H), 3.89 (d, J = 6.2 Hz, 1H), 3.78 (d, J = 5.8 Hz, 1H), 3.69 (dd, J = 6.3, 12.1 Hz, 1H), 3.65-3.64 (m, 1H), 3.56-3.32 (m, 15H), 3.29 (dd, J = 6.6, 12.5 Hz, 1H), 3.29-3.23 (m, 3H), 3.00-2.99 (m, 2H), 2.87-2.82 (m, 2H), 2.74 (t, J = 9.5Hz, 1H), 2.28 (s, 3H, -C(O)CH3), 1.98 (s, 3H, -C(O)CH3), 1.37-1.22 (m, 4H, -CCH2C-), 1.07-1.00 (m, 2H, -CCH2C-); 13C NMR (150 MHz, CDCl3): δ 171.29, 169.57, 168.78, 168.58, 168.03, 167.90, 139.01, 138.92, 138.84, 138.68, 138.45, 138.39, 138.36, 138.22, 138.14, 137.98, 134.35, 134.15, 134.02, 133.89, 132.04, 131.95, 131.68, 130.10, 129.54, 129.46, 128.80, 128.70, 128.66, 128.62, 128.60, 128.52, 128.47, 128.46, 128.39, 128.30, 128.15, 128.07, 128.01, 127.98, 127.94, 127.91, 127.83, 127.72, 127.60, 127.39, 127.20, 126.96, 123.90, 123.46, 122.88, 101.11, 100.87, 98.87, 98.33, 83.75, 80.57, 80.14, 78.58, 78.29, 76.15, 75.78, 75.45, 74.11, 74.96, 74.83, 74.70, 74.61, 74.44, 74.10, 73.77, 73.73, 73.59, 73.43, 73.38, 73.03, 72.30, 71.97, 70.61, 70.29, 69.82, 69.14, 69.08, 68.54, 68.38, 67.94, 66.94, 66.47, 63.21, 56.80, 56.09, 56.01, 51.37, 31.71, 31.21, 30.97, 30.59, 29.99, 29.65, 28.55, 27.87, 27.29, 26.96, 26.24, 25.59, 25.36, 24.26, 23.27, 22.98, 21.86, 21.32, 20.80, 20.49, 18.94, 16.76, 15.95, 15.44, 15.10, 14.40, 14.07, 13.67, 13.47; ESI-MS: m/z calcd for C153H156N6O36; 1327.0189; found 1350.0207 (M +Na)+.
Figure imgf000176_0001
[00466] 5-Azidopentyl-O-{2-O-acetyl-3,4,6-O-tri-benzyl-β-D-galactopyranosyl-(1→4)}-O- {3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→2)}-O-{3,4,6-tri-O- benzyl-α-D-mannopyranosyl-(1→3)-{2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl- (1→3)}-[2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→6)]-2,4-di-O-benzyl-α-D- manno-pyranosyl-(1→6)}-2-O-acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2- deoxy-2-phthalimido-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2- phthalimido-β-D-glucopyranoside (S12c): A mixture of hexasaccharide acceptor S12b (0.40 g, 0.15 mmol), thiomannoside donor 3 (0.229 g, 0.226 mmol) and activated 4 Å molecular sieves (0.50 g) in CH3CN (10 mL) was stirred at rt for 1 h. The resulting mixture was cooled to -10 °C, tris (4-bromophenyl)aminium hexachloroantimonate (0.254 g, 0.30 mmol) was added and stirred at rt for 3 h. TLC indicated formation of product with consumption of starting material, the reaction was then quenched by Et3N. The reaction mixture was diluted with CH2Cl2 and filtered through celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S12c (0.335 g, 55%) as colorless foam and acceptor 9 (0.103 g). TLC: (ethyl acetate: toluene = 1/9, v/v): Rf = 0.46; 1H NMR (600 MHz, CDCl3): δ 7.72- 7.45 (m, 11H, Ar-H), 7.37-7.28 (m, 5H, Ar-H), 7.28-7.12 (m, 67H, Ar-H), 7.09-7.02 (m, 12H, Ar-H), 6.94-6.90 (m, 7H, Ar-H), 6.80-6.78 (m, 4H, Ar-H), 6.696.68 (m, 3H, Ar-H), 6.62-6.61 (m, 3H, Ar-H), 5.49 (s, 1H), 5.48 (s, 1H), 5.35 (t, J = 8.4 Hz, 1H), 5.28 (d, J = 8.4 Hz, 1H, H-1), 5.17 (d, J = 8.4 Hz, 1H, H-1), 5.09 (d, J = 6.2 Hz, 1H), 5.00 (s, 1H, H-1), 4.92 (d, J = 3.1 Hz, 1H), 4.90-4.72 (m, 12H), 4.69-4.72 (m, 23H), 4.26-4.17 (m, 5H), 4.133.97 (m, 12H), 3.89-3.82 (m, 12H), 3.72 (t, 1H), 3.68-3.62 (m, 1H), 3.65-3.55 (m, 7H), 3.54-3.45 (m, 4H), 3.43-3.40 (m, 4H), 3.40-3.29 (m, 9H), 3.23-3.19 (m, 3H), 3.17-3.09 (m, 2H), 2.91-2.79 (m, 3H), 2.68 (s, 1H), 2.28 (s, 3H, -C(O)CH3), 2.05 (s, 3H, -C(O)CH3), 2.01 (s, 3H, - C(O)CH3), 1.99 (s, 3H, -C(O)CH3), 1.34-1.22 (m, 4H, linker), 1.06-1.00 (m, 2H, linker); 13C NMR (150 MHz, CDCl3): δ 171.37, 170.38, 170.29, 169.54, 168.49, 168.23, 167.97, 167.53, 139.28, 139.11, 139.03, 138.97, 138.94, 138.67, 138.63, 138.58, 138.53, 138.41, 138.38, 138.25, 138.10, 128.74, 128.70, 128.67, 128.63, 128.58, 128.55, 128.53, 128.51, 128.48, 128.44, 128.40, 128.37, 128.34, 128.30, 128.15, 128.03, 128.00, 127.95, 127.92, 127.84, 127.77, 127.75, 127.70, 127.64, 127.61, 101.17, 100.92, 98.84, 98.28, 97.71, 97.45, 75.49, 75.36, 75.26, 75.17, 75.06, 74.96, 74.82, 74.75, 74.65, 74.60, 74.38, 74.30, 73.99, 73.77, 73.73, 73.59, 73.25, 73.25, 73.06, 72.99, 72.91, 72.26, 72.18, 71.98, 71.82, 71.57, 71.45, 70.52, 70.03, 69.92, 69.56, 69.10, 68.90, 68.85, 68.57, 68.48, 68.37, 66.64, 66.06, 56.75, 56.09, 55.99, 51.37, 34.25, 29.99, 28.94, 28.54, 25.90, 23.27, 21.86, 21.42, 21.33; HRMS (MALDI-TOF): m/z calcd for C231H238N6O53; 3945.6071; found 3968.6006 (M + Na)+.
Figure imgf000178_0001
[00467] 5-Aminopentyl-β-D-galactopyranosyl-(1→4)-[2-acetamido-2-deoxy-β-D-gluco- pyranosyl-(1→2)-α-D-mannopyranosyl-(1→3),[di-(α-D-mannopyranosyl)-(1→3),(1→6)-α- D-manno-pyranosyl](1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-gluco- pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G12): Compound S12c (0.16 g, 0.048 mmol) was deprotected by following general procedure 2 (Method 1) to afford desired the nonasaccharide G12 (0.052 g, 62% ). 1H NMR (600 MHz, D2O): δ 5.10 (s, 1H, H-1d), 5.07 (d, J = 9.5 Hz, 1H, H-1a), 4.91 (s, 2H, H-1h,h'), 4.84 (s, 1H, H-1f), 4.61(s, 1H, H- 1c), 4.50 (d, J = 9.2 Hz, 1H, H-1b), 4.49 (d, J = 8.1 Hz, 1H, H-1e), 4.31 (s, 2H), 4.19 (bs, 1H), 4.07 (bs, 1H), 4.023.51 (m, 53H), 3.40-3.30 (m, 2H) 2.99 (t, J = 11.2 Hz, 2H, -NCH2-, linker), 2.08 (s, 3H, -C(O)CH3), 2.07 (s, 3H, -C(O)CH3), 2.04 (s, 3H, -C(O)CH3), 1.70–1.65 (m, 2H, -CCH2C-, linker), 1.62-1.58 (m, 2H, -CCH2C-, linker), 1.48–1.38 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 177.60, 177.17, 105.68 (C-1b), 105.05 (C-1d), 104.23, 104.04, 103.79, 103.37, 103.18, 102.88, 102.23 (C-1h'), 102.03 (C-1h), 100.24 (C- 1g), 82.20, 82.06, 82.01, 81.58, 81.51, 81.40, 79.38, 78.70, 78.08, 77.43, 77.37, 77.18, 77.03, 76.07, 75.66, 75.43, 75.23, 75.11, 75.06, 74.96, 74.83, 74.71, 73.72, 73.65, 73.33, 73.20, 73.11, 72.95, 72.89, 72.84, 72.69, 72.18, 71.28, 70.15, 68.50, 69.46, 69.36, 69.01, 68.31, 67.90, 67.86, 64.45, 63.75, 63.69, 63.61, 62.87, 62.82, 62.75, 57.94, 57.72, 42.06, 30.78, 29.10, 25.35, 25.30, 24.96, 24.87, 24.83; ESI-MS: m/z calcd for C65H112N4O46; 1684.6620 found 1685.6968 (M + H)+.
Figure imgf000179_0001
[00468] 5-Aminopentyl-5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-[2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl-(1→3),[di-(α-D-mannopyranosyl)-(1→3),(1→6)-α-D-manno- pyranosyl] (1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G13): Compound G12 (5 mg, 0.0029 mmol) was sialylated with α-2,6-sialyltransferase for 2 days by following general procedure 3 to get the desired title compound G13 (3.5 mg, 60%) as white solid. 1H NMR (600 MHz, D2O): δ 5.07 (s, 1H, H-1d), 5.06 (d, J = 8.5 Hz, 1H, H-1a), 4.92 (s, 1H, H-1h), 4.90 (s, 1Hi), 4.89 (s, 1H, H-1i'), 4.78 (s, 1H, H-1c), 4.58 (d, J = 7.2 Hz, 1H, H-1f), 4.46 (d, J = 7.8 Hz, 1H, H-1b), 4.41 (d, J = 8.4 Hz, 1H, H-1e), 4.25-4.24 (m, 2H), 4.12 (s, 1H), 4.04 (d, J = 4.7 Hz, 1H), 4.04-3.42 (m, 61H), 3.40 (t, J = 10.8 Hz, 1H), 3.39-3.35 (m, 1H), 2.95 (t, J = 10.9 Hz, 2H), 2.64 (dd, J = 4.2, 12.2 Hz, 1H, H-3equi. g), 2.04 (s, 3H, -C(O)CH3), 2.04 (s, 3H, - C(O)CH3), 2.00 (s, 3H, -C(O)CH3), 2.00 (s, 3H, -C(O)CH3), 1.71-1.61 (m, 3H, -CCH2C-, linker and H-3axial g), 1.58-1.54 (m, 2H, -CCH2C-, linker), 1.39-1.35 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.90, 174.79, 174.38, 173.47, 103.42, 102.29 (C- 1d, 1 J C,H = 170.9 Hz), 101.48, 101.01, 100.41, 100.18 (C-1a, 1 J C,H = 162.9 Hz), 100.15, 99.24 ((C-1h, 1 J C,H = 171.3 Hz)), 97.87, 97.27, 80.78, 79.59, 79.20, 78.72, 78.36, 76.61, 75.81, 74.79, 74.48, 74.36, 73.63, 73.28, 72.63, 72.52, 72.35, 72.30, 72.09, 71.94, 71.65, 70.82, 70.69, 70.53, 70.31, 70.12, 70.05, 69.89, 69.41, 68.33, 68.17, 67.32, 67.17, 66.66, 65.47, 65.09, 63.30, 62.62, 61.66, 60.98, 60.89, 60.32, 60.02, 59.94, 57.95, 54.91, 51.81, 40.01, 39.27, 28.00, 26.37, 23.62, 23.19, 22.59, 22.17, 22.05, 22.00; ESI-MS (negative mode): m/z calcd for C76H129N5O54; 1975.7418 found 1974.7600 (M -H)-.
[00469] 5-Aminopentyl-5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→3)-β-D-galactopyranosyl-(1→4)-[2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl-(1→3),[di-(α-D-mannopyranosyl)-(1→3),(1→6)-α-D-manno- pyranosyl] (1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G14): Compound G12 (5 mg, 0.0029 mmol) was sialylated with α-2,3-sialyltransferase for 8 d by following general procedure 3 to get the desired title compound G14 (3.1 mg, 56%) as white solid. 1H NMR (600 MHz, D2O): δ 5.01 (s, 1H, H-1d), 4.97 (dd, J = 3.2, 7.2 Hz, 1H, H-1a), 4.84 (s, 1H, H-1h), 4.81 (s, 1H, H-1i), 4.75 (s, 1H, H-1i'), 4.62 (s, 1H, H-1c), 4.52 (d, J = 7.8 Hz, 1H, H-1f), 4.97 (d, J = 9.2 Hz, 1H, H-1b), 4.42 (d, J = 8.3 Hz, 1H, H-1e), 4.39 (d, J = 8.3 Hz, 1H), 4.22 (t, J = 7.8 Hz, 2H), 4.09 (s, 1H), 4.06 (d, J = 7.4 Hz, 1H), 4.03 (d, J = 7.3 Hz, 1H), 4.00 (d, J = 3.2 Hz, 1H), 3.96-3.85 (m, 10H), 3.85-3.71 (m, 19H), 3.72-3.52 (m, 26H), 3.51-3.48 (m, 2H,), 3.38- 3.370 (m, 2H), 2.90 (t, J = 7.9 Hz, 2H, -NCH2-, linker), 2.68 (dd, J = 4.8, 12.0 Hz, 1H, H-3 equi. g), 2.01 (s, 3H, -C(O)CH3), 1.99 (s, 3H, -C(O)CH3), 1.96 (s, 3H, -C(O)CH3), 1.95 (s, 3H, -C(O)CH3), 1.73 (t, J = 8.6 Hz, 1H, H-3 axial g), 1.61-1.56 (m, 2H, -CCH2C-, linker), 1.54-1.46 (m, 2H, -CCH2C-, linker), 1.34-1.33 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 171.94, 171.81, 171.37, 170.80, 113.44, 99.86, 99.53, 99.27, 98.42, 97.99, 97.38, 97.08, 96.74, 96.21, 75.74, 75.66, 75.52, 73.56, 72.85, 72.41, 72.10, 71.62, 71.45, 71.36, 70.27, 69.81, 69.62, 69.28, 69.14, 69.02, 68.90, 68.69, 67.91, 67.82, 67.50, 67.20, 67.08, 66.87, 66.36, 65.46, 65.29, 65.01, 64.39, 64.32, 63.68, 62.47, 62.09, 61.02, 59.50, 59.39, 58.64, 57.96, 57.87, 57.10, 56.91, 52.12, 51.91, 48.60, 42.85, 40.32, 36.54, 36.25, 35.04, 25.27, 24.98, 23.34, 20.60, 19.53, 19.13, 19.03, 18.95, 13.70; ESI-MS (negative mode): m/z calcd for C76H129N5O54; 1975.7418 found 1974.7671 (M - H)-.
00470 Pre aration of l cans G9-G11
Figure imgf000181_0001
[00471] Scheme S13 | Preparation of G9-G11. i) (1) NH2CH2CH2NH2, n-BuOH, 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2; 51%; ii) CMP-β-D-Sialic acid, α-2,6/2,3- sialyltransferase,G10: 77%;G11: 52%
Figure imgf000182_0001
[00472] 5-Aminopentyl-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl (1→2)-α-D-mannopyranosyl]-(1→3)-β-D-mannopyranosyl-(1→4)-2- acetamido-2-deoxy-βD-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G10): Hexasaccharide S12a (0.110 g, 0.041 mmol) was deprotected following general procedure 2 (Method 1) to get the desired compound G10 (0.025 g, 51% ) as white solid. 1H NMR (600 MHz, D2O): δ 5.04 (d, J = 8.4 Hz, 1H, H-1a), 4.84 (s, 1H, H-1d), 4.78 (s, 1H, H- 1c), 4.60 (d, J = 8.2 Hz, 1H, H-1e), 4.51 (d, J = 8.1 Hz, 1H, H-1b), 4.46 (d, J = 7.8 Hz, 1H, H- 1f), 4.28 (d, J = 3.3 Hz, 1H), 4.26 (d, J = 3.6 Hz, 1H), 4.10-3.82 (m, 9H), 3.82-3.56 (m, 23H), 3.52-3.38 (m, 5H), 2.97 (t, J = 7.8 Hz, 2H, - NCH2-, linker), 2.07 (s, 3H, -C(O)CH3), 2.05 (s, 3H, -C(O)CH3), 2.03 (s, 3H, -C(O)CH3), 1.701.65 (m, 2H, -CCH2C-, linker), 1.62-1.58 (m, 2H, -CCH2C-, linker), 1.48-1.41 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 177.64, 177.32, 177.17, 173.74, 105.65, 104.13, 103.80, 103.18, 102.70, 100.08, 82.05, 81.50, 81.37, 79.38, 79.04, 78.85, 78.09, 77.42, 77.28, 77.24, 75.23, 75.13, 75.06, 74.80, 74.67, 73.69, 72.84, 71.27, 70.14, 70.07, 68.12, 64.43, 63.74, 63.61, 62.85, 62.82, 62.75, 57.91, 57.78, 57.73, 42.05, 30.78, 29.10, 25.27, 24.87, 24.85, 24.83; ESI-MS: m/z calcd for C47H82N4O3; 1198.4855 found 1221.5223 (M + Na)+.
Figure imgf000183_0001
[00473] 5-Aminopentyl-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl]-(1→3)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β- D-gluco-pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G10): Compound G9 (10 mg, 0.0083 mmol) was sialylated with α-2,6-sialyltransferase for 2 days by following general procedure 3 to get the desired title compound G10 (9.5 mg, 77%) as white solid. 1H NMR (600 MHz, D2O): δ 5.06 (d, J = 7.8 Hz, 1H, H-1a), 4.80 (s, 1H, H-1d), 4.78 (s, 1H, H- 1c), 4.60 (d, J = 7.8 Hz, 1H, H-1e), 4.49 (d, J = 7.8 Hz, 1H, H-1b), 4.43 (d, J = 7.8 Hz, 1H, H- 1f), 4.27 (d, J = 3.6 Hz, 1H), 4.25 (d, J = 3.6 Hz, 1H), 4.08-3.38 (m, 45H), 2.98 (t, J =11.2 Hz, 2H, -NCH2-, linker), 2.60 (dd, J = 4.8, 12.0 Hz, 1H, H-3 equi. g), 2.08 (s, 6H, - C(O)CH3) 2.05 (s, 3H, -C(O)CH3), 2.03 (s, 3H, -C(O)CH3, 1.71 (t, J = 7.8Hz, 1H, H-3 axial g), 1.69-1.69 (m, 2H, -CCH2C-, linker), 1.611.56 (m, 2H, -CCH2C-, linker), 1.41-1.37 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.94, 174.83, 174.56, 174.40, 103.50, 101,37, 101.03, 100.31, 100.12, 99.92, 97.31, 80.99, 79.28, 78.63, 78.59, 76.61, 76.32, 76.07, 74.51, 74.48, 74.38, 73.67, 72.52, 72.38, 72.36, 72.08, 71.90, 71.66, 70.70, 70.06, 68.37, 68.34, 67.33, 63.35, 62.63, 61.67, 60.88, 60.09, 59.98, 54.99, 54.87, 51.85, 40.02, 39.30, 28.01, 26.36, 22.56, 22.10, 22.08, 21.99; ESI-MS (negative mode): m/z calcd for C58H99N5O39; 1489.5833 found 1488.5949 (M - H)-.
Figure imgf000184_0001
[00474] 5-Aminopentyl-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→3)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl]-(1→3)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β- D-gluco-pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (G11): Compound G9 (7 mg, 0.0058 mmol) was sialylated with α-2,3-sialyltransferase for 4 days by following general procedure 3 to get desired the title compound G11 (4.6 mg, 52%) as white solid. 1H NMR (600 MHz, D2O): δ 5.06 (d, J = 8.4 Hz, 1H, H-1a), 4.79 (s, 1H, H-1d), 4.75 (s, 1H, H- 1c), 4.62 (d, J = 6.6 Hz, 1H, H-1e), 4.56 (d, J = 7.8 Hz, 1H, H-1b), 4.51 (d, J = 7.8 Hz, 1H, H- 1f), 4.28 (d, J = 8.4 Hz, 2H), 4.13 (d, J = 9.6 Hz, 1H), 3.99-3.83 (m, 12H), 3.82-3.57 (m, 27H), 3.53-3.39 (m, 4H), 2.99 (t, J = 7.8 Hz, 2H), 2.77 (dd, J = 4.8, 2.0 Hz, 1H, H-3 equi. g), 2.12 (s, 3H, -C(O)CH3) 2.09 (s, 3H, -C(O)CH3), 2.05 (s, 3H, -C(O)CH3), 2.03 (s, 3H, - C(O)CH3), 1.80 (t, J = 7.8 Hz, 1H, H-3 axial g), 1.71-1.66 (m, 2H, -CCH2C-, linker), 1.62- 1.59 (m, 2H, -CCH2C-, linker), 1.44-1.41 (m, 2H, -CCH2C-, linker); 13C NMR (150 MHz, D2O): δ 174.88, 174.53, 174.46, 174.40, 102.50, 102,37, 101.65, 101.31, 100.12, 99.86, 98.31, 80.32, 79.67, 78.78, 78.56, 76.66, 75.32, 75.07, 74.51, 74.48, 74.38, 73.67, 72.52, 72.38, 72.36, 72.08, 71.90, 71.66, 70.70, 70.06, 68.37, 68.34, 67.33, 63.35, 62.63, 61.67, 60.88, 60.09, 59.98, 54.99, 54.87, 51.85, 40.02, 39.30, 28.01, 26.36, 22.56, 22.10, 22.08, 21.2720.27; ESI-MS (negative mode): m/z calcd for C58H99N5O39; 1489.5833 found 1488.5944(M - H)-.
[00475] Synthesis of complex type oligosaccharides S
Figure imgf000185_0001
Figure S3 | Structures of complex type glycans. [00476] Previously, we have developed an efficient chemo-enzymatic strategy for the rapid production of bi-(G15, G16, and G17), tri- (G20-G22, G23, G25 and G26) and tetraantennary (G28, G32 and G33) complex type N-glycans, with and without terminal N-acetylneuraminic acid residues connected via the α-2,6 or α-2,3 linkages. In addition, we have developed a total chemical synthesis strategy which utilized a modular set of glycosyl donors (1-13) for stereo- and region-selective glycosylation to core trisaccharide 15. However, the synthesis of assymetrically sialylated glycans by enzyme is complicated by their specificity. For this reason, we demonstrated the utility of glycosyl fluoride to prepare assymetric complex type glycans. Intitially, we started with pthallamide protections at C2-amine of all glucosamine residues of both antennae and core trisaccharides (14), however, in presence of preinstalled sialic acid, the process of global deprotection was found to be complicated. To overcome this difficulty, the pthallamide protections at C2-amine of all glucosamine residues were replaced with trichloroethyl carbonate (troc).
[00477] Synthesis of glycan G18.
[00478] Glycosylation of sialylated antenne 9 with core 15 at 3-O site provided desired heptasaccharide S14a in 63% yield. Benzylidene was removed in the presence of p-TSA to get 4,6-diol S14b, which was further alpha glycosylated at 6-O position with 8 to afford desired S14c as mixture of α and β forms (7/3 isolated yield). The major α isomer was isolated by column chromatography and finally deprotected to get G18 as a white solid.
Figure imgf000186_0001
[00479] Scheme S14 | Preparation of G18. i, 9, AgOTf, Cp2HfCl2, toluene, -20 °C to O °C, 63%; ii, pTSA, acetonitrile, 59%; iii, 8, AgOTf, Cp2HfCl2, toluene, -40 °C to -20 °C, 58%; iv, (1) LiOH, 1, 4-dioxane: H2O, 90 °C, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd (OH)2, MeOH: H2O, H2, 25%.
Figure imgf000186_0002
[00480] Compound S14a: A mixture of silver triflate (0.087 g, 0.34 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.090 g, 0.23 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -20 °C, a solution of donor 9 (0.153 g, 0.082 mmol) and acceptor chitobiose trisaccharide 15 (0.100 g, 0.068 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h at 0 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% acetone in toluene) to afford S14a (0.140 g, 63%) as white foam. TLC: (acetone: toluene = 1.5/8.5, v/v): Rf = 0.52; 1H NMR (600 MHz, CDCl3): δ 7.89 (d, J = 7.8 Hz, 4H), 7.49-7.46 (m, 2H), 7.37-7.06 (m, 59H), 5.77 (t, J = 10.8 Hz, 1H), 5.35-5.37 (m, 2H), 5.26 (s, 1H), 5.18 (dd, J = 3.8 & 7.7 Hz, 1H), 5.08 (d, J = 3.2 Hz, 1H), 5.07 (dd, J = 3.2 & 8.4 Hz, 1H), 4.97 (d, J = 8.4 Hz, 1H), 4.91 (d, J = 9.1 Hz, 1H), 4.86 (d, J = 8.7 Hz, 3H), 4.73-4.13 (m, 32H), 4.02-3.30 (m, 29H), 3.20 (t, J = 10.8 Hz, 2H), 3.10 (d, J = 8.7 Hz, 1H), 2.98 (t, J = 9.2 Hz, 1H), 2.87-2.85 (m, 1H), 2.80 (dd, J = 3.2 & 7.8 Hz, 1H), 2.10 (s, 6H), 2.08 (t, J = 9.3 Hz, 1H), 2.00 (s, 6H), 1.40-1.17 (m, 4H), 0.87-0.82 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.9, 170.8, 170.2, 170.0, 167.9, 166.1, 165.5, 159.5, 154.5, 154.3, 154.1, 138.2, 130.1, 129.8, 129.6, 129.4, 128.9, 128.8, 128.7, 128.6, 128.5, 128.4, 128.3, 128.2, 128.1, 127.9, 127.8, 127.6, 127.0, 100.8, 100.5, 98.0, 95.8, 76.8, 76.7, 75.5, 74.8, 74.6, 74.4, 74.3, 74.1, 73.8, 73.7, 73.4, 73.2, 69.9, 69.7, 69.5, 68.7, 67.5, 66.7, 61.9, 58.9, 57.6, 53.4, 37.4, 29.9, 29.2, 28.8, 23.4, 21.3, 21.2, 21.0, 20.9, 14.3; ESI-MS: m/z calcd for C160H172Cl9N7O48; 3278.8343 found 3278.8127.
Figure imgf000187_0001
[00481] Compound S14b: p-Toluene sulfonic acid monohydrate (0.004 g, 0.022 mmol) was added to a solution of S14a (0.150 g, 0.045 mmol) in acetonitrile (20 mL) and the resulting reaction mixture was stirred at room temperature for 5h. The reaction was quenched by adding Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% EA in toluene) to give diol S14b (0.085 g, 59%). TLC:
(acetone: toluene = 2/8, v/v): Rf = 0.32 NMR (600 MHz, CDCl3): δ 7.89-7.86 (m, 4H), 7.49- 7.37 (m, 2H), 7.30-7.09 (m, 54H), 5.78 (t, J = 10.2 Hz, 1H), 5.51 (d, J = 7.8 Hz, 1H), 5.37 (dt, J = 2.4 & 7.2 Hz, 1H), 5.26 (s, 1H), 5.19 (dd, J = 2.4 & 10.8 Hz, 1H), 5.12 (d, J = 3.6 Hz, 1H), 4.95-4.85 (m, 5H), 4.75-4.12 (m, 25H), 4.08-4.03 (m, 3H), 3.96-3.89 (m, 7H), 3.74-3.67 (m, 8H), 3.63-3.30 (m, 20H), 3.20 (t, J = 10.2 Hz, 2H), 3.10 (d, J = 8.9 Hz, 2H), 2,89 (s, 1H), 2.76 (dd, J = 3.6 & 7.9 Hz, 1H), 2.08 (s, 3H), 2.05 (s, 3H), 1.99 (s, 3H), 1.95 (s, 3H), 1.41- 1.31 (m, 5H), 1.27-1.17 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 172.4, 172.3, 171.3, 171.2, 170.7, 170.3, 170.0, 168.4, 168.3, 166.1, 165.5, 154.5, 154.3, 154.1, 153.9, 138.5, 138.4, 138.1, 138.0, 133.7, 133.3, 130.1, 129.8, 129.7, 129.5, 129.3, 128.9, 128.8, 128.7, 128.6, 128.6, 128.5, 128.4, 128.3, 128.2, 128.1, 128.0, 127.9, 101.1, 100.8, 100.6, 100.4, 99.7, 99.2, 96.0, 95.8, 76.3, 76.1, 75.7, 75.5, 74.9, 74.8, 74.5, 74.3, 74.0, 73.7, 73.4, 73.3, 73.2, 73.1, 73.0, 72.6, 72.3, 72.1, 71.3, 71.0, 69.9, 69.6, 69.4, 69.3, 68.4, 67.8, 66.1, 66.2, 62.8, 62.2, 59.2, 57.7, 53.4, 51.5, 36.9, 29.9, 29.2, 28.8, 25.0, 23.4, 21.4, 21.3, 21.2, 21.1, 15.5, 14.4; ESI-MS (negative mode): m/z calcd for C153H168Cl9N7O48; 3191.8105 found 3236.8033 (M + 2Na)-.
Figure imgf000188_0001
[00482] Compound S14c: A mixture of silver triflate (0.067 g, 0.27 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.071 g, 0.18 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 8 (0.097 g, 0.068 mmol) and acceptor S14b (0.175 g, 0.054 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h at -20 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 10% acetone in toluene) to separate mixture of α and β isomers to afford S14c (0.149 g, 58%) as white foam. TLC: (acetone: toluene = 1.5/8.5, v/v): Rf = 0.52; 1H NMR (600 MHz, CDCl3): δ 7.90 (d, J = 7.2 Hz, 2H), 7.83 (d, J = 7.8 Hz, 2H), 7.51-7.41 (m, 4H), 7.34-7.06 (m, 92H), 5.83 (t, J = 10.2 Hz, 1H), 5.48-5.03 (m, 3H), 5.00-4.75 (m, 13H), 4.60-4.08 (m, 41H), 3.99-3.07 (m, 53H), 2.96 (t, J = 10.2 Hz, 2H), 2.80 (dd, J = 3.8 & 7.9 Hz, 1H), 2.15 (s, 3H), 2.10 (s, 3H), 2.07 (s, 3H), 2.00 (s, 3H), 1.93 (s, 3H), 1.40-1.17 (m, 5H), 0.91-0.81 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 170.9, 170.6, 170.4, 169.9, 169.4, 166.5, 159.5, 154.7, 154.4, 139.8, 138.8, 138.7, 138.6, 138.4, 138.2, 133.7, 130.9, 130.7, 129.7, 129.6, 129.4, 129.2, 129.0, 128.7, 128.6, 128.6, 128.4, 128.3, 128.2, 127.9, 127.6, 127.3, 100.4, 100.2, 99.8, 99.4, 74.9, 74.7, 74.5, 73.3, 73.2, 66.1, 60.6, 51.5, 32.1, 29.8, 29.7, 29.6, 29.3, 28.7, 23.7, 22.8, 22.4, 22.0, 21.6, 21.4, 21.2, 20.9, 15.4, 14.3, 14.2, 14.0, 11.3, 10.2; ESI-MS: m/z calcd for C232H250Cl12N8O65; 4607.2765 found 2330.6261 (M + Na) 2+.
Figure imgf000189_0001
[00483] 5-Aminopentyl-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl]-(1→3),-[β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy- β-D-glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl-(1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside G18: Compound S14c (0.135 g, 0.029 mmol) was deprotected by following general procedure 2 (method 2) to afford the desired glycan G18 (0.015 g, 25%). 1H NMR (600 MHz, D2O): δ 5.11 (s, 1H, H-1d), 4.89 (s, 1H, H-1d'), 4.73 (s, 1H, H-1c), 4.57 (dt, J = 10.2 Hz, 2H, H-1f,f'), 4.47 (d, J = 7.8 Hz, 2H, H-1a,b), 4.47 (d, J = 8.4 Hz, 2H, H-1e,e'), 4.23 (s, 1H), 4.17 (s, 1H), 4.09 (d, J = 1.3 Hz, 1H), 4.03-3.48 (m, 61H), 2.98 (t, J = 10.2 Hz, 2H, - CH2- linker), 2.65 (dd, J = 4.8 & 12.6 Hz, 1H, H-3equi. g), 2.10 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 2.02 (s, 6H), 1.72-1.64 (m, 3H, H-3axial g, linker -CH2-), 1.63-1.54 (m, 2H), 1.39-1.35 (m, 2H); 13C NMR (150 MHz, D2O): δ 177.7, 177.5, 177.4, 177.1, 176.2, 176.1, 106.2, 106.1, 104.1, 103.7, 103.5, 103.1, 102.9, 102.9, 99.5, 83.6, 83.1, 82.2, 82.1, 81.7, 79.4, 79.1, 78.9, 77.3, 77.2, 76.8, 76.4, 75.3, 75.1, 74.8, 74.5, 73.5, 73.4, 72.8, 71.2, 70.9, 70.0, 67.6, 66.0, 65.6, 65.4, 64.5, 62.8, 57.7, 57.3, 55.0, 54.6, 54.0, 42.8, 42.3, 42.0, 41.78, 30.7, 30.5; ESI-MS (negative mode): m/z calcd for C78H132N6O542016.7767; found 1007.3799 (M - H)2-.
[00484] Synthesis of glycan G24.
[00485] Compound S14b acts as common acceptor for both G18 and G24. Glycosylation of S14b at 6-O site provided the desired S15a with 10% acceptor recovery. At last, global deprotection yielded the desired glycan G24.
Figure imgf000191_0001
[00486] Scheme S15 | Preparation of G24. i, 12, AgOTf, Cp2HfCl2, toluene, -40 °C, 63%; ii, (1) LiOH, 1, 4-dioxane, 90 °C, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd(OH)2, MeOH: H2O, H2, 42%.
Figure imgf000191_0002
[00487] Compound S15a: A mixture of silver triflate (0.058 g, 0.23 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.061 g, 0.23 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 12 (0.135 g, 0.056 mmol) and acceptor S14b (0.150 g, 0.046 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h at -20 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 10% acetone in toluene) to afford S15a (0.165 g, 63%) as white foam. TLC: (acetone: toluene = 1.5/8.5, v/v): Rf = 0.58; 1H NMR (600 MHz, CDCl3): δ 8.00-7.80 (m, 4H), 7.50-6.80 (m, 116H), 5.80 (t, J = 10.2 Hz, 1H), 5.40-5.30 (m, 7H), 5.10- 4.08 (m, 65H), 4.00-3.05 (m, 65H), 2.98 (dd, J = 3.2 & 8.5 Hz, 1H), 2.15 (s, 6H), 2.10 (s, 6H), 2.00 (s, 6H), 1.37-1.17 (m, 5H), 0.87-0.84 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 170.8, 167.9154.1, 139.1, 139.0, 138.9, 138.8, 138.6, 138.3, 138.1, 138.0, 129.8, 129.6, 129.3, 128.9, 128.8, 128.7, 128.7, 128.6, 128.5, 128.4, 128.2, 128.0, 127.7, 127.4, 127.3, 127.2, 127.1, 127.0, 100.8, 100.0, 74.9, 74.8, 74.5, 74.4, 73.6, 73.3, 72.6, 53.5, 29.9, 29.2, 23.4, 21.3, 21.2, 21.0, 20.9, 15.5, 14.4; ESI-MS (negative mode): m/z calcd for
C277H298Cl15N9O77; 5517.1670 found 2803.7442 (M + 2Na)2-.
Figure imgf000192_0001
[00488] 5-Aminopentyl-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→2)-α-D-mannopyranosyl]-(1→3),-[β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy- β-D-glucopyranosyl-(1→2), (1→6)-α-D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl- (1→4)2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside G24: Compound S15a (0.090 g, 0.016 mmol) was deprotected by following general procedure 2 (method 2) to afford desired glycan G24 (0.016 g, 42%) as a white solid. 1H NMR (600 MHz, D2O): δ 5.14 (s, 1H, H-1d), 4.88 (s, 1H, H-1d'), 4.60 (t, J = 10.2 Hz, 3H, H- 1e,f,e'), 4.55 (d, J = 8.4 Hz, 1H), 4.48 (dd, J = 3.2 & 8.6 Hz, 4H), 4.45 (d, J = 7.8 Hz, 1H), 4.26 (s, 1H), 4.20 (s, 1H), 4.09 (s, 1H), 4.01-3.50 (m, 71H), 2.97 (t, J = 10.2 Hz, 2H, linker -CH2-), 2.68 (dd, J = 3.8 & 8.3 Hz, 1H, H-3equi. g), 2.08 (s, 3H, -C(O)CH3), 2.07 (s, 3H, -C(O)CH3), 2.04 (s, 3H, -C(O)CH3), 2.03 (s, 6H, -C(O)CH3), 1.72 (t, J = 10.2 Hz, 1H, H-3axial g), 1.67-1.65 (m, 2H), 1.60-1.56 (m, 2H, linker -CH2-), 1.40-1.39 (m, 2H, linker - CH2-); 13C NMR (150 MHz, D2O): δ 174.9, 174.7, 174.6, 174.5, 174.4, 174.1, 173.5, 103.6, 103.5, 102.9, 102.8, 101.5, 101.4, 101.0, 100.3, 100.1, 99.5, 99.3, 80.7, 80.4, 79.5, 79.3, 79.2, 78.5, 76.5, 75.4, 75.2, 74.7, 74.5, 74.4, 74.3, 73.7, 73.4, 72.5, 72.4, 72.3, 72.1, 71.9, 71.6, 71.3, 70.9, 70.8, 70.5, 70.3, 69.5, 69.4, 68.5, 68.3, 68.2, 67.5, 67.3, 65.4, 63.3, 62.5, 61.7, 61.0, 60.2, 60.1, 59.8, 55.08, 54.9, 54.8, 54.6, 51.0, 40.9, 39.4, 28.0, 26.7, 22.5, 22.4, 22.3, 22.2, 22.1, 22.0, 21.09 ; ESI-MS (negative mode): m/z calcd for C92H155N7O64; 2383.2370 found 1213.4483 (M + Na)2-.
[00489] Synthesis of glycan G25.
Figure imgf000194_0001
[00490] Scheme S16 | Preparation of G25. i, 12, AgOTf, Cp2HfCl2, toluene, -40 °C, 64%; ii, pTSA, acetonitrile, 56%; iii, 8, AgOTf, Cp2HfCl2, toluene, -78 °C, 49%; iv, (1) LiOH, 1,4- dioxane, 90 °C, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd(OH)2, MeOH: H2O, H2, 38%.
Figure imgf000194_0002
[00491] Compound 16a: A mixture of silver triflate (0.087 g, 0.34 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.090 g, 0.23 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -40 °C, a solution of donor 12 (0.259 g, 0.082 mmol) and acceptor 15 (0.100 g, 0.068 mmol) in 5 mL toluene was added. The mixture was stirred for 3 h at -10 o C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 20% acetone in toluene) to afford S16a (0.201 g, 64%) as white foam. TLC: (acetone: toluene = 2.5/7.5, v/v): Rf = 0.50; 1H NMR (600 MHz, CDCl3): δ 7.92-7.83 (m, 9H), 7.69-7.67 (m, 2H), 7.52-7.44 (m, 6H), 7.37-6.96 (m, 63H), 5.345.32 (m, 2H), 5.26-5.24 (m, 4H), 5.20-5.10 (m, 3H), 5.08 (d, J = 9.8 Hz, 3H), 4.59-4.40 (m, 8H), 4.75- 4.50 (m, 20H), 4.49-4.00 (m, 20H), 3.98-3.60 (m, 16H), 3.48-3.06 (m, 16H), 2.98 (t, J = 10.7 Hz, 2H), 2.76 (dd, J = 3.8 & 7.8 Hz, 2H), 2.08 (s, 3H), 2.07 (s, 3H), 2.06 (s, 6H), 1.99 (s, 9H), 1.37-1.17 (m, 6H), 0.89-0.84 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.8, 171.7, 171.6, 169.8, 169.4, 168.0, 167.6, 166.6, 166.4, 166.2, 165.4, 165.3, 159.7, 159.4, 154.3, 154.2, 139.8, 139.7, 139.6, 139.4, 139.2, 138.7, 138.6, 138.5, 138.4, 138.3, 138.2, 133.9, 132.7, 131.9, 131.2, 130.6, 129.8, 129.6, 129.4, 129.3, 129.2, 129.0, 128.8, 128.7, 128.6, 128.6, 128.4, 128.2, 128.1, 128.0, 127.9, 127.8, 127.7, 127.6, 127.5, 127.4, 127.3, 127.2, 127.0, 102.7, 102.4, 101.9, 101.8, 100.8, 100.7, 100.4, 100.2, 100.0, 99.2, 99.4, 98.4, 96.5, 95.9, 74.3, 74.1, 74.0, 73.8, 73.7, 73.5, 73.4, 73.2, 73.1, 72.7, 72.5, 72.1, 71.3, 70.9, 70.4, 69.5, 69.4, 68.5, 68.4, 68.3, 68.1, 67.9, 67.4, 53.4, 51.6, 37.5, 33.9, 32.2, 31.8, 29.9, 28.8, 26.5, 23.4, 22.9, 21.2, 21.0, 20.0, 14.6, 14.3; ESI-MS: m/z calcd for C220H235Cl12N9O72; 4582.6910 found 915.6684 (M + H)5+.
Figure imgf000196_0001
[00492] Compound 16b: p-Toluene sulfonic acid monohydrate (0.002 g, 0.008 mmol) was added to a solution of S14a (0.200 g, 0.043 mmol) in acetonitrile (10 mL) and resulting reaction mixture was stirred at rt for overnight. Reaction was quenched by adding Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 20% acetone in toluene) to give diol S16b (0.110 g, 56%). TLC: (acetone: toluene = 2.5/7.5, v/v): Rf = 0.32; 1H NMR (600 MHz, CDCl3): δ 7.90-7.80 (m, 7H), 7.79 (d, J = 8.4 Hz, 2H), 7.69-7.46 (m, 5H), 7.41-7.04 (m, 65H), 5.78 (t, J = 10.1 Hz, 1H), 5.73 (t, J = 10.7 Hz, 1H), 5.35-5.25 (m, 7H), 5.20 (dd, J = 3.2 & 7.9 Hz, 1H), 5.15 (dd, J = 3.8 & 8.4 Hz, 1H), 5.08 (t, J = 10.8 Hz, 2H), 4.90-4.80 (m, 5H), 4.794.50 (m, 15H), 4.48-4.30 (m, 8H), 4.20-4.10 (m, 15H), 3.92-3.20 (m, 35H), 3.2 (t, J = 8.8 Hz, 2H), 3.18-3.05 (m, 3H), 3.0-2.95 (m, 3H), 2.81- 2.70 (m, 3H), 2.08 (s, 6H), 2.07 (s, 6H), 2.03 (s, 6H), 1.92 (s, 6H), 1.32-1.17 (m, 6H), 0.89- 0.83 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.8, 170.7, 168.0, 166.1, 159.6, 138.1, 133.7, 132.7, 131.1, 130.1, 129.9, 129.7, 129.4, 128.9, 128.8, 128.7, 128.6, 128.4, 128.3, 128.2, 127.8, 127.7, 127.6, 74.9, 74.7, 74.6, 73.9, 68.8, 66.1, 53.4, 51.6, 37.3, 32.4, 31.4, 29.9, 29.8, 29.7, 28.7, 28.4, 23.4, 22.3, 20.9, 20.7, 20.4, 15.5, 14.6, 14.2 ; ESI-MS: m/z calcd for C213H231Cl12N9O72; 4494.5820 found 681.2953 (M + K)7+.
Figure imgf000197_0001
[00493] Compound 16c: A mixture of silver triflate (0.068 g, 0.34 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.065 g, 0.17 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -78 °C, a solution of donor 8 (0.109 g, 0.076 mmol) and acceptor 16b (0.230 g, 0.051 mmol) in 5 mL toluene was added. The mixture was stirred for 3 h at -20 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 20% acetone in toluene) to afford S16c (0.148 g, 49%) as white foam. TLC: (acetone: toluene = 2.5/7.5, v/v): Rf = 0.50; 1H NMR (600 MHz, CDCl3): δ 7.90 (m, 10H), 7.52-6.80 (m, 110H), 5.79 (t, J = 10.2 Hz, 2H), 5.48 (dd, J = 4.2 & 8.7 Hz, 2H), 5.34-5.14 (m, 10H), 4.98-3.10 (m, 129H), 2.85 (t, J = 10.2 Hz, 2H), 2.30 (dd, J = 3.4 & 8.2 Hz, 2H), 2.01 (s, 3H), 2.00 (s, 6H), 1.95 (s, 6H), 1.94 (s, 6H), 1.91 (s, 3H), 1.39-1.29 (m, 6H), 1.26-1.91 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 172.1, 170.8, 170.3, 170.1, 170.0, 169.3, 169.2, 168.0, 167.3, 166.5, 165.8, 165.1, 165.0, 154.0, 153.8, 153.7, 153.7, 139.0, 138.9, 138.8, 138.7, 138.6, 138.3, 138.2, 138.1, 137.9, 137.4, 133.4, 133.2, 132.0, 130.3, 129.8, 129.7, 129.4, 129.3, 129.2, 129.1, 128.9, 128.8, 128.5, 128.3, 128.2, 128.1, 128.0, 127.9, 100.4, 100.2, 99.3, 75.8, 75.6, 75.4, 75.3, 75.2, 75.1, 74.8, 74.7, 74.6, 74.5, 74.4, 74.3, 74.2, 74.2, 74.1, 73.5, 73.4, 73.3, 73.2, 73.1, 73.0, 72.9, 72.6, 72.2, 71.9, 71.7, 71.6, 71.3, 71.1, 70.1, 69.9, 69.8, 68.5, 68.3, 68.2, 63.4, 58.8, 58.3, 58.0, 53.4, 51.3, 31.9, 30.3, 30.0, 29.8, 29.7, 29.5, 28.7, 28.5, 28.3, 27.1, 24.5, 24.1, 23.8, 22.7, 22.1, 21.7, 20.9, 20.7, 20.6, 14.1, 14.0, 10.9 ; ESI-MS (negative mode): m/z calcd for C292H313Cl15N10O89;
5918.4470 found 1486.4746 (M + 6H)4+.
Figure imgf000198_0001
[00494] 5-Aminopentyl-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→2),(1→4)-α-D-mannopyranosyl]-(1→3),-[β-D-galactopyranosyl-(1→4)- 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→6)-β-D- mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2- deoxy-β-D-glucopyranoside G25: Compound S16c (0.115 g, 0.019 mmol) was deprotected by following general procedure 2 (method 2) to afford the desired glycan G25 (0.020 g, 38%).1H NMR (600 MHz, D2O): δ 5.15 (d, 1H, H-1d), 4.94 (s, 1H, H-1d'), 4.63 (d, J = 8.4 Hz, 2H, H-1a,b), 4.58 (d, J = 7.8 Hz, 2H, H-1e,e'), 4.52 (d, J = 7.8 Hz, 2H, H-1e",f'), 4.50 (s, 1H, H-1c), 4.42 (dd, J = 3.2 & 10.2 Hz, 2H, H-1f,f"), 4.23 (s, 2H), 4.08 (s, 1H), 3.92 (dd, J = 3.2 & 7.8 Hz, 2H), 3.90-3.45 (m, 75H), 3.01 (t, J = 10.2 Hz, 2H, linker CH2), 2.69 (dd, J = 3.6 & 12.1 Hz, 2H, H-3equi.g,g'), 2.12 (s, 3H), 2.10 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 2.05 (s, 9H), 1.77-1.66 (m, 4H, H-3axial.g,g' and linker CH2), 1.62-1.60 (m, 2H), 1.42-1.40 (m, 2H) ; 13C NMR (150 MHz, D2O): δ 177.6, 177.4, 177.3, 177.1, 176.1, 106.3, 105.6, 104.2, 104.1, 103.7, 103.1, 102.8, 102.1, 101.8, 99.8, 78.7, 78.0, 77.4, 77.2, 77.176.4, 75.5, 75.2, 75.1, 75.0, 74.8, 74.4, 74.0, 73.7, 73.4, 73.0, 72.8, 72.1, 71.5, 70.9, 70.8, 70.0, 68.4, 66.0, 65.4, 64.3, 64.0, 63.7, 63.1, 63.8, 62.6, 57.7, 57.6, 57.5, 57.3, 54.6, 42.7, 42.0, 30.7, 29.0, 25.3, 25.0, 24.9, 24.8, 24.7; ESI-MS (negative mode): m/z calcd for C103H172N8O72; 2674.4930 found 1335.9948 (M - 2H)2-.
[00495] Synthesis of glycan G29.
[00496] Glycan G29 is mono sialylated tetraantennary complex type structure. The synthesis began with construction of D1 arm by glycosylation of donot 11 at 3-O position of 15 to afford compound S17a. The reaction was progress was checked by TLC as shown in Scheme S17. Removal benzyledene followed by 6-O glycosylation afforded desired tetra- decasaccharide S17c. Finally, global deprotection provided desired glycan G29.
Figure imgf000199_0001
[00497] Scheme S17 | Preparation of G29. i, 11, AgOTf, Cp2HfCl2, toluene, -40 °C, 77%; ii, pTSA, acetonitrile, 73%; iii, 13, AgOTf, Cp2HfCl2, toluene, -40 °C, 57%; iv, (1) LiOH, 1,4- dioxane, 90 °C, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd(OH)2, MeOH: H2O, H2, 34%.
Figure imgf000200_0001
[00498] Compound S17a: A mixture of silver triflate (0.173 g, 0.675 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.177 g, 0.469 mmol) and 4 Å activated molecular sieves in dry toluene (10 mL) was stirred at room temperature for 1 h. The reaction mixture was then cooled to -50 °C, a solution of donor 11 (0.345 g, 0.470 mmol) and acceptor 15 (0.195 g, 0.134 mmol) in 5 mL toluene was added. The mixture was stirred for 2 h at -10 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% acetone in toluene) to afford S17a (0.380 g, 77%) as white foam. TLC: (acetone: toluene = 1/9, v/v): Rf = 0.60 NMR (600 MHz, CDCl3): δ 7.30- 7.12 (m, 60H), 7.08-6.72 (m, 25H), 5.39 (t, J = 10.2 Hz, 1H ), 5.29 (t, J = 10.3 Hz, 1H'), 5.16 (d, J = 4.2 Hz, 1H), 5.09 (d, J = 8.4 Hz, 1H), 4.91-4.72 (m, 18H, overlapped), 4.63-4.56 (m, 5H), 4.01-4.80 (m, 30H), 3.80-3.95 (m, 10H), 3.60-3.75 (m, 4H), 3.52-3.48 (m, 6H), 3.41- 3.15 (m, 20H), 2.98 (d, J = 9.6Hz, 1H), 2.90-2.76 (m, 3H), 2.662.62 (m, 1H), 1.95 (s, 3H), 1.93 (s, 3H), 1.87 (s, 3H), 1.38-1.23 (m, 4H, -CCH2C-), 1.08-1.01 (m, 2H, -CCH2C-); 13C NMR (150 MHz, CDCl3): δ 172.1, 171.9, 170.5, 156.7, 156.6, 142.0, 141.8, 141.6, 141.5, 141.4, 141.3, 141.3, 141.1, 140.8, 140.6, 140.5, 139.8, 135.2, 133.6, 133.2, 131.8, 131.5, 131.3, 131.1, 130.6, 130.5, 130.2, 130.1, 129.8, 129.0, 127.3, 104.8, 104.8, 103.2, 102.9, 77.7,77.5,77.3, 77.2, 77.1, 76.9, 76.2, 76.1, 76.0, 75.9, 75.5, 75.4, 74.8,, 74.6, 74.5, 74.4, 74.3, 71.0, 70.8, 70.6, 54.0, 31.7, 31.3, 25.9, 23.9, 23.8, 23.7, 23.6, 17.2, 17.1, 16.8, 16.7, 13.7, 13.6; HRMS (negative mode): m/z calcd for C190H205Cl12N7O48; 3778.9981 found 3824.9969 (M + 2Na)-.
Figure imgf000201_0001
[00499] Compound S17b: p-Toluene sulfonic acid monohydrate (0.004 g, 0.02 mmol) was added to a solution of S17a (0.377 g, 0.102 mmol) in acetonitrile (10 mL) and the resulting reaction mixture was stirred at rt for overnight. The reaction was quenched by adding Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0% → 10% acetone in toluene) to give diol S17b (0.270 g, 73%). TLC: (acetone: toluene = 1.5/8.5, v/v): Rf = 0.32; 1H NMR (600 MHz, CDCl3): δ 7.34-7.11 (m, 80H), 5.37 (s, 1H), 5.29 (t, J = 10.2 Hz, 1H), 5.22 (t, J = 9.8 Hz, 1H), 5.02 (d, J = 3.6 Hz, 2H), 4.92-4.74 (m, 7H), 4.70-4.21 (m, 34H), 3.93-3.51 (m, 17H), 3.65-3.20 (m, 30H), 3.20 (t, J = 10.2 Hz, 4H), 2.98 (d, J = 3.8 Hz, 2H), 2.89 (s, 1H), 2.11 (s, 3H), 1.94 (s, 3H), 1.90 (s, 3H), 1.40-1.17 (m, 4H), 091-0.84 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 170.1, 170.0, 169.6, 168.0, 154.3, 154.1, 139.6, 139.1, 139.0, 138.9, 138.7, 138.5, 138.3, 138.1, 138.0, 132.7, 131.1, 129.6, 129.4, 129.3, 129.0, 128.7, 128.6, 128.5, 128.4, 128.3, 128.2, 128.1, 128.0, 127.9, 127.6, 127.5, 127.3, 127.1, 127.0, 100.9, 100.6, 100.5, 98.6, 95.9, 95.8, 76.75, 76.3, 75.6, 74.8, 74.6, 74.5, 74.3, 74.2, 73.8, 73.7, 73.5, 73.2, 72.8, 72.5, 72.1, 69.6, 68.8, 68.5, 68.4, 68.2, 68.1, 62.8, 62.1, 57.6, 39.0, 37.3, 33.7, 32.5, 31.4, 30.6, 29.9, 29.2, 28.8, 26.6, 24.0, 23.4, 23.2, 22.9, 21.5, 21.3, 20.1, 15.5, 14.6, 14.4, 14.3, 11.2; HRMS (negative mode): m/z calcd for
C183H201Cl12N7O48; 3692.0222 found 3737.9645 (M + 2Na)2-.
Figure imgf000202_0001
[00500] Compound S17c: A mixture of silver triflate (0.046 g, 0.180 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.048 g, 0.126 mmol) and 4 Å activated molecular sieves in dry toluene (5 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -50 °C, a solution of donor 13 (0.100 g, 0.36 mmol) and acceptor S17b (0.118 g, 0.032 mmol) in 5 mL toluene was added. The mixture was stirred for 3 h at -10 o C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 10% actone in toluene) to afford S17c (0.120 g, 57%) as white foam. TLC: (acetone: toluene = 1/9, v/v): Rf = 0.60; 1H NMR (600 MHz, CDCl3): δ 7.58-7.54 (m, 6H), 7.50-6.98 (m, 134H), 5.57 (t, J = 10.3 Hz, 4H), 5.42-5.30 (m, 24H), 5.01-4.70 (m, 35H), 4.65-4.10 (m, 50H), 4.0-2.90 (m, 52H), 2.80 (d, J = 9.8 Hz, 2H), 2.15 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 1.96 (s, 3H), 1.93 (s, 3H), 1.88 (s, 3H), 1.86 (s, 3H), 1.34-1.17 (m, 5H), 0.89- 0.81 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 139.1, 139.0, 138.3, 138.2, 138.1, 130.1, 129.9, 129.1, 129.0, 128.9, 128.8, 128.7, 128.6, 128.4, 128.3, 128.1, 128.0, 127.9, 127.8, 127.6, 127.4, 74.8, 74.6, 73.7, 73.6, 71.9 ; HRMS (negative mode): m/z calcd for
C322H346Cl18N10O89; 6418.3910 found 3253.3555 (M + 2Na)2-.
Figure imgf000203_0001
[00501] 5-Aminopentyl-di-[β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2),(1→4)-α-D-mannopyranosyl]-(1→3),-[5-Acetamido-3,5-dideoxy-D- glycero-α-D- galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2- acetamido-2- deoxy-β-D-glucopyranosyl-(1→6)-β-D-galactopyranosyl-(1→4)-2-acetamido- 2-deoxy-β-D- glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside G29: Compound S17c (0.095 g, 0.015 mmol) was deprotected by following general procedure 2 (method 2) to afford desired glycan G29 (0.014 g, 34%) as a white powder. 1H NMR (600 MHz, D2O): δ 4.99 (s, 1H, H-1d), 4.75 (s, 1H, H-1d’), 4.72 (d, J = 8.4 Hz, 1H, H-1e), 4.62 (d, 1H, J = 7.8 Hz, 1H, H-1e’), 4.63 (s, 1H, H-1c), 4.45 (dd, J = 3.6 & 7.8 Hz, 4H, H-1e”,e’”, f,f’), 4.36-4.31 (m, 4H), 4.09 (s, 3H), 3.98-3.04 (m, 85H), 2.83 (t, J = 10.2 Hz, 2H, linker), 2.56 (dd, J = 3.2 & 8.4 Hz, 1H, H-3equi. g'), 1.95 (s, 3H, -C(O)CH3), 1.94 (s, 3H, -C(O)CH3), 1.93 (s, 3H, -C(O)CH3), 1.92 (s, 3H, -C(O)CH3), 1.92 (s, 3H, - C(O)CH3), 1.90 (s, 3H, -C(O)CH3), 1.89 (s, 3H, - C(O)CH3), 1.61-1.42 (m, 5H, H-3axial g' and linker CH2), 1.30-1.24 (m, 2H, linker); 13C NMR (150 MHz, D2O): δ 186.6, 174.7, 174.3, 174.2, 103.3, 102.7, 101.8, 100.8, 99.9, 98.5, 97.3, 78.9, 78.1, 77.8, 75.1, 74.4, 74.2, 74.1, 72.2, 71.7, 71.5, 70.7, 69.8, 68.3, 68.1, 63.1, 62.4, 60.8, 60.2, 59.7, 54.9, 54.6, 51.6, 39.9, 39.1, 27.8, 26.1, 22.2, 21.8, 17.6; ESI-MS (negative mode): m/z calcd for
C106H178N8O74; 2747.0411 found 1396.0177 (M + Na)2-.
[00502] Synthesis of glycan G30.
[00503] Depicted in Scheme S18, precussor S16b from scheme S16 was used as acceptor for 6-O glycosylation with donor 11 under the promotion of silver triflate and hafnocene dichloride to obtain the desired S18a. The final deprotection provided the disialylated tetra- antennary complex glycan G30.
Figure imgf000204_0001
[00504] Scheme S18 | Preparation of G30. i, 11, AgOTf, Cp2HfCl2, toluene, -40 °C, 37%; ii, (1) LiOH, 1, 4-dioxane, 90 °C, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd(OH)2, MeOH:H2O, H2, 45%.
Figure imgf000205_0001
[00505] Compound S18a: A mixture of silver triflate (0.051 g, 0.200 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.053 g, 0.140 mmol) and 4 Å activated molecular sieves in dry toluene (5 mL) was stirred at room temperature for 1 h. The reaction mixture was then cooled to -50 °C, a solution of donor 11 (0.144 g, 0.060 mmol) and acceptor S16b (0.180 g, 0.040 mmol) in 5 mL toluene was added. The mixture was stirred for 3 h at -10 °C, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% acetone in toluene) to afford S18a (0.103 g, 37%) as white foam. TLC: (acetone: toluene = 2/8, v/v): Rf = 0.53; 1H NMR (600 MHz, CDCl3): δ 7.69-7.52 (m, 20H), 7.33-7.06 (m, 130H), 5.60 (m, 17H), 4.80-4.30 (m, 40H), 4.20-4.00 (m, 50H), 3.99-3.02 (m, 25H), 2.08 (s, 9H), 2.07 (s, 6H), 2.05 (s, 6H), 2.02 (s, 6H), 1.78-1.74 (m, 6H), 0.91-0.84 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 170.9, 170.4, 170.2, 169.8, 169.4, 169.3, 132.7, 131.1, 129.0, 128.7, 128.4, 128.3, 128.2, 128.0, 127.8, 127.7, 127.6, 127.5, 68.8, 68.4, 39.0, 37.3, 33.7, 31.4, 30.6, 29.9, 29.2, 26.6, 26.0, 24.0, 23.2, 22.9, 20.1, 14.6, 14.2, 11.40; ESI-MS (negative mode): m/z calcd for C337H361Cl18N11O101; 6806.6710 found 723.5969 (M + K)10-.
Figure imgf000206_0001
[00506] 5-Aminopentyl-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2),(1→4)-α-D-mannopyranosyl]-(1→3),-di-[-β-D-galactopyranosyl- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→6),(1→2)-α-D-mannopyranosyl]- (1→6)-β-D- mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2- acetamido-2- deoxy-β-D-glucopyranoside G30: Compound S18a (0.075 g, 0.010 mmol) was deprotected by following general procedure 2 (method 2) to afford desired glycan G30 (0.015 mg, 45%). 1H NMR (600 MHz, D2O): δ 5.12 (s, 1H, H-1d), 4.86-4.74 (m, 3H, H-1d', c, b, overlapped with D2O),4.59-4.55 (m, 5H, H-1e,e',e",e'",a), 1.48-4.42 (m, 4H, H-1f,f',f",f'"), 4.21-4.06 (m, 5H), 3.98-3.3.20 (m, 91H), 2.98 (t, J = 10.7 Hz, 2H, linker CH2), 2.66 (dd, J = 3.7 & 10.1 Hz, 2H, 2 x H-3equi.g,g'), 2.12 (s, 3H), 2.09 (s, 3H, -C(O)CH3), 2.06 (s, 3H, - C(O)CH3), 2.05 (s, 3H, -C(O)CH3), 2.03 (s, 12H, - C(O)CH3), 1.75-1.54 (m, 6H, 2 x H- 3axial.g,g' and linker CH2), 1.42-1.36 (m, 2H, linker); 13C NMR (150 MHz, D2O): δ 174.7, 174.2, 174.1, 103.4, 102.7, 101.3, 101.2, 101.0, 100.8, 100.6, 99.9, 98.9, 97.9, 78.1, 75.1, 74.3, 73.4, 72.3, 72.1, 71.7, 70.7, 70.4, 69.8, 68.3, 68.0, 59.9, 59.7, 54.7, 51.6, 39.9, 27.8, 22.7, 22.0, 21.9, 21.8; ESI-MS (negative mode): m/z calcd for C117H195N9O82; 3039.8280 found 1518.5585 (M - H)2-. [00507] Synthesis of glycan G31.
[00508] Intermidiate S16b derived from scheme S16 was used for α-selective glycosylation using donor 13 in presence of AgOTf/Cp2HfCl2 to get S19a in 74% yield. However, the newly formed product was overlaped with acceptor on TLC (Scheme S19). S19a was then further deprotected to furnish glycan G31.
Figure imgf000207_0001
[00509] Scheme S19 | Preparation of G31. i, 13, AgOTf, Cp2HfCl2, toluene, -50 oC, 74%; ii, (1) LiOH, 1,4-dioxane, 90 oC, (2) Ac2O, pyridine, (3) NaOMe, MeOH, (4) Pd(OH)2, MeOH: H2O, H2, 47%.
Figure imgf000207_0002
[00510] Compound S19a: A mixture of silver triflate (0.042 g, 0.165 mmol), bis
(cyclopentadienyl) hafnium dichloride (0.043 g, 0.115 mmol) and 4 Å activated molecular sieves in dry toluene (5 mL) was stirred at rt for 1 h. The reaction mixture was then cooled to -50 °C, a solution of donor 13 (0.100 g, 0.036 mmol) and acceptor S16b (0.150 g, 0.033 mmol) in 5 mL toluene was added. The reaction mixture was stirred for 2 h at -20 oC, quenched with Et3N, diluted with EtOAc and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and a brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% acetone in toluene) to afford S19a (0.183 g, 74%) as white foam. TLC: (acetone: toluene = 2/8, v/v): Rf = 0.50; 1H NMR (600 MHz, CDCl3): δ 7.90-7.83 (m, 9H), 7.69-7.67 (m, 3H), 7.57-7.50 (m, 3H), 7.38-7.04 (m, 125H), 5.77 (t, J = 10.2 Hz, 4H), 5.54-5.40 (m, 20H), 5.39 (t, J = 8.4 Hz, 4H), 5.08 (t, J = 7.8 Hz, 4H), 4.98-4.60 (m, 25H), 4.53-4.42 (m, 31H), 4.30-4.10 (m, 35H), 4.00-3.80 (m, 42H), 3.21-3.18 (m, 64H), 2.93-2.78 (m, 4H), 2.08 (s, 6H), 2.07 (s, 6H), 2.05 (s, 3H), 2.02 (s, 3H), 1.98 (s, 6H), 1.94 (s, 6H), 1.74-1.18 (m, 7H), 0.91-0.84 (m, 2H); 13C NMR (150 MHz, CDCl3): δ 171.8, 171.7, 170.8, 169.9, 169.8, 168.5, 168.0, 166.1, 165.4, 159.5, 132.7, 131.7, 130.1, 129.9, 129.2, 128.9, 128.8, 128.7, 128.6, 128.4, 128.3, 128.2, 128.1, 128.0, 127.9, 127.8, 127.7, 127.6, 127.5, 100.7, 100.6, 100.4, 95.8, 74.9, 74.6, 74.2, 73.9, 73.7, 73.6, 73.2, 72.9, 72.2, 71.9, 71.0, 70.5, 69.3, 68.5, 68.3, 68.0, 67.3, 66.1, 65.3, 62.3, 61.2, 53.4, 51.5, 39.0, 37.3, 33.7, 32.4, 32.2, 30.6, 29.9, 29.6, 29.4, 29.3, 28.8, 26.6, 24.0, 23.9, 23.5, 23.4, 23.1, 21.2, 20.1, 15.5, 14.6, 14.4, 14.3, 11.2; HRMS (negative mode): m/z calcd for C352H376Cl18N12O113; 7220.9510 found 3654.9220 (M + 2Na)2-.
Figure imgf000209_0001
[00511] 5-Aminopentyl-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2),(1→4)-α-D-mannopyranosyl]-(1→3),-[ 5-Acetamido-3,5-dideoxy-D- glycero-α-D- galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2- acetamido-2- deoxy-β-D-glucopyranosyl-(1→6)- β-D-galactopyranosyl-(1→4)-2-acetamido- 2-deoxy-β-D- glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside G31: Compound S19a (0.180 g, 0.024 mmol) was deprotected by following general procedure 2 (method 2) to afford desired glycan G31 (0.039 g, 47%). 1H NMR (600 MHz, D2O): δ 5.12 (s, 1H, H-1d), 4.87 (s, 2H, H-1d',c), 4.75 (d, J = 8.4 Hz, 2H, H-1b, e), 5.59-4.55 (m, 5H, overlapped H- 1a, e', e'", e"", f), 4.49-4.42 (m, 5H, overlapped H-1f'-f""), 4.21-4.19 (m, 4H), 4.06-3.54 (m, 95H), 2.97 (t, J = 10.2 Hz, 2H, linker -CH2), 2.66 (dd, J = 3.2 & 7.8 Hz, 3H, H-3g,g',g'"equi), 2.09 (s, 3H), 2.06 (s, 9H), 2.04 (s, 3H), 2.02 (s, 12H), 1.74 (m, 2H, linker), 1.64 (t, J = 10.2 Hz, 3H, H-3g,g',g'"axial), 1.59-1.57 (m, 2H, linker), 1.39-1.37 (m, 2H, linker); 13C NMR (150 MHz, D2O): δ 174.8, 174.7, 174.5, 174.4, 174.3, 174.1, 173.3, 103.5, 102.9, 101.7, 101.4, 101.2, 100.2, 100.0, 99.8, 99.6, 99.3, 80.8, 80.6, 80.3, 79.3, 78.4, 78.3, 76.7, 75.3, 74.3, 74.2, 74.1, 74.0, 73.8, 72.9, 72.8, 72.6, 72.4, 72.3, 72.2, 72.1, 72.0, 71.9, 71.7, 71.3, 70.8, 70.4, 70.3, 70.2, 68.4, 68.4, 63.4, 62.9, 60.4, 60.3, 60.2, 59.8, 54.8, 54.3, 54.2, 51.8, 51.0, 43.7, 43.3, 39.8, 39.5, 34.4, 27.5, 26.3, 22.6, 22.4, 22.4, 22.2, 22.0, 21.9 ; ESI-MS (negative mode): m/z calcd for C128H212N10O90;
3331.0840 found 1664.1108 (M - H)2-.
[00512] Synthesis of core fucosylated glycans G3 and G19 S
[00513] The pauci mannose type structure bearing core fucose G312 was assembled from the reducing end disaccharide S20k through fucosylation of diol acceptor S20j by donor S20i (Scheme S20). The α-selectivity was enhanced by in situ anomarization protocol (CuBr2, tetrabutyl ammonium bromide), which was first developed by Lemieux and co-workers14, to get disaccharide S20k in 67% yield with its regio- and stereo-chemistry confirmed by NMR analysis. The formation of the key β-mannosyl linkage using sulfoxide donor S20a13 and acceptor S20b was performed using DTBP and Tf2O to get disaccharide S20c in 67% yield with α/β ratio of 1:7. The p-methoxy benzyl ether protection at 3" was removed by using DDQ to afford 3"-OH S20d, which was further subjected to 3"-O α-mannosylation by using imidate 1 under the promotion of BF3.OEt2 to obtained trisaccharide S20e. Selective benzylidene opening of S20e produced S20f, which further underwent α-mannosylation at 6"- O position to get tetrasaccharide S20g. Compound S20g was then converted into glycosyl imidate S20h by treatment with PdCl2 and then trichloroacetimidate and DBU. Finally the condensation of imidate S20h and disaccharide S20k12 in the presence of BF3.OEt2 provided desired hexasaccharide S20i. The global deprotection afforded the paucimannose type oligosaccharide G3.
Figure imgf000211_0001
[00514] Scheme S20 | Preparation of glycan G3. i, DTBP, Tf2O, CH2Cl2, -60 oC, 3 h, 67% (α/β 1:7); ii, DDQ, CH2Cl2 : H20 = 10/1, 3 h, 70%; iii, 1, BF3.OEt2, CH2Cl2, 4 Å MS, -40 oC, 1 h, 81%; iv, Triethyl sillane, PhBCl2, CH2Cl2, 1 h, 73%; v, BF3.OEt2, CH2Cl2, 4 Å MS, -20°C, 2 h, 65%; vi, (i) PdCl2, MeOH:CH2Cl2, RT, 6 h, (ii) DBU, trichloroacetonitrile, CH2Cl2, 63% over 2 steps; vii, Cu(II)Br, TBAB, DMF:CH2Cl2, 4 Å MS,0°C to RT, overnight, 76%; viii, BF3.OEt2, CH2Cl2, 4 Å MS,-70 oC, 2 h, 45%; ix, (i)
NH2CH2CH2NH2, nBuOH, 100 oC; (ii) Ac2O, pyridine, 0 oC to RT; (iii) NaOMe, MeOH; (iv) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2, 22% over 4 steps. TBAB = Tetrabutyl ammonium bromide.
Figure imgf000211_0002
[00515] Allyl-O-2-O-benzyl-3-O-p-methoxy-benzyl-4,6-O-benzylidine-β-D- mannopyranosyl-(1→4)- O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S20c): A mixture of donor S20a (0.272 g, 0.483 mmol) and activated 4 Å molecular sieves (0.5 g) in CH2Cl2 (10 mL) was stirred at rt for 1 h. The reaction mixture was cooled to -60 oC, 2,6-di-ter-butyl pyridine (268 µL, 1.24 mmol) followed by Tf2O (79 µL, 0.483 mmol) was added and stirred for 40 minutes. A solution of acceptor S20b (0.2 g, 0.378 mmol) in CH2Cl2 (5 mL) was added slowly and the resulting reaction mixture was stirred for 1 h until TLC (ethyl acetate: toluene, 1/9) indicated formation of a product with consumption of the starting material. The reaction mixture was quenched with Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S20c (0.230 g, 67%) as white solid. TLC: (ethyl acetate: toluene = 1/9, v/v): Rf = 0.52; 1H NMR (600 MHz, CDCl3): δ 7.65-7.45 (m, 8H, Ar-H), 7.35-7.21 (m, 13H, Ar-H), 6.91-6.90 (m, 2H, Ar-H), 6.90-6.81 (m, 5H, Ar-H), 5.67-5.65 (m, 1H, allyl), 5.49 (s, 1H, Ph-CH, benzylidene), 5.13 (d, J = 8.4 Hz, 1H, H-1a), 5.07 (d, J = 8.8 Hz, 1H), 4.99 (d, J = 10.4 Hz, 1H), 4.87-4.82 (m, 3H), 4.65 (d, J = 5.4 Hz, 1H), 4.63 (d, J = 5.4 Hz, 1H), 4.53 (s, 1H), 4.50 (d, J = 12.0 Hz, 1H), 4.41 (d, J = 6.0 Hz, 1H), 4.39 (d, J = 6.0 Hz, 1H), 4.24-4.21 (m, 2H), 4.05-3.96 (m, 3H), 3.81 (s, 3H, OMe of PMB), 3.71 (d, J = 3.0 Hz, 1H), 3.64 (d, J = 10.8 Hz, 1H), 3.56-3.52 (m, 2H), 3.45-3.47 (d, J = 10.0 Hz, 1H), 3.40 (dd, J = 3.0, 6.6 Hz, 1H), 3.13-3.12 (m, 1H); 13C NMR (150 MHz, CDCl3): δ 159.46, 139.08, 138.99, 138.12, 138.00, 134.05, 130.93, 129.37, 129.22, 128.84, 128.60, 128.54, 128.47, 128.45, 128.26, 128.12, 128.09, 128.07, 127.83, 127.21, 126.41, 117.60, 114.04, 102.28, 101.63, 97.70, 79.85, 78.99, 78.33, 77.44, 75.29, 75.03, 74.95, 73.86, 72.61, 69.99, 68.86, 68.84, 67.66, 55.96, 55.58; ESI-MS: m/z calcd for C59H59NO13: 989.3879; found 1012.3888 (M + Na)+.
Figure imgf000213_0001
[00516] Allyl-O-2-O-benzyl-4,6-O-benzylidine-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O- benzyl-2- deoxy-2-phthalimido-β-D-glucopyranoside (S20d): To a solution of S20c (0.5 g, 0.505 mmol) in 10 mL CH2Cl2: H2O (10:1) was added DDQ (0.219g, 1.01 mmol) at 0 °C and the resulting reaction mixture was stirred for 3 h. The reaction mixture was then filtered, organic layer washed with H2O (2 x 30 mL). The aqueous layer was further extracted with CH2Cl2 (2 x 50 mL). The combined organic layers were washed with brine solution (40 mL), dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S20d (0.308 g, 70%) as colorless foam. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.42; 1H NMR (600 MHz, CDCl3): δ 7.65-7.44 (m, 6H, Ar-H), 7.43-7.28 (m, 13H, Ar-H), 6.92-6.90 (m, 2H, Ar-H), 6.83-6.81 (m, 3H, Ar-H), 5.68-5.64 (m, 1H, Allyl), 5.42 (s, 1H, Ph-CH, benzylidene), 5.14 (d, J = 8.4 Hz, 1H, H-1a), 5.08 (d, J = 12.8 Hz, 1H), 5.01-4.98 (m, 2H), 4.85 (d, J = 12.6 Hz, 1H), 4.74 (d, J = 12.0 Hz, 1H), 4.65 (d, J = 12.0 Hz, 1H), 4.62 (s, 1H, H-1b), 4.84 (d, J = 12.0 Hz, 1H), 4.40 (d, J = 12.0 Hz, 1H), 4.25-4.16 (t, J = 9.6 Hz, 1H), 3.99 (dd, J = 13.0 & 6.3 Hz, 1H), 3.73-3.65 (m, 4H), 3.54-3.47 (m, 3H), 3.13-3.09 (m, 1H); 13C NMR (150 MHz, CDCl3): 138.97, 138.44, 137.93, 137.56, 133.98, 129.37, 128.92, 128.79, 128.53, 128.43, 128.35, 128.26, 128.21, 128.10, 127.99, 127.27, 126.58, 117.64, 102.33, 102.25, 97.66, 79.91, 79.42, 79.15, 77.43, 76.00, 75.03, 74.89, 74.01, 71.24, 69.99, 68.78, 68.67, 67.17, 55.90; ESI-MS: m/z calcd for C51H51NO12: 869.3303; found 892.3314 (M + Na)+.
Figure imgf000214_0001
[00517] Ally-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2-O-benzyl-4,6- O- benzylidine-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β- D- glucopyranoside (S20e):- A mixture of donor 1 (0.537 g, 0.863 mmol), acceptor S20d (0.50 g, 0.574 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at rt for 30 minutes. The reaction was cooled to -40 oC, boron trifluoride ethyl etherate (32 µL, 0.288 mmol) was then added slowly and the resulting reaction mixture was stirred for 1 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0% → 20% EA in hexane) to afford S20e (0.630 g, 81%) as colorless oil. TLC: (ethyl acetate: hexane = 3/7, v/v): Rf = 0.62; 1H NMR (600 MHz, CDCl3): δ 7.41-7.39 (m, 4H, Ar-H), 7.39-7.25 (m, 30H, Ar-H), 7.16-6.82 (m, 5H, Ar- H), 5.57-5.57 (m, 1H, Allyl), 5.59 (d, J = 3.0 Hz, 1H), 5.47 (s, 1H, Ph-CH, benzylidene), 5.29 (d, J = 2.1 Hz, 1H, H-1c), 5.13 (d, J = 8.4 Hz, 1H, H-1a), 5.08 (dd, J = 6.0 & 12.2 Hz, 1H), 5.00 (dd, J = 6.0, 10.2 Hz, 1H), 4.87- 4.82 (m, 2H), 4.79-4.78 (m, 2H), 4.66-4.59 (m, 3H), 4.54 (s, 1H, H- 1b), 4.46-4.44 (m, 3H), 4.22-4.20 (m, 2H), 4.17-4.14 (m, 2H), 4.03-3.93 (m, 4H), 3.82-3.71 (m, 5H), 3.64-3.62 (m, 2H), 3.60-3.52 (m, 2H), 3.50 (d, J = 8.2Hz, 1H), 3.19 (m, 1H), 2.34 (s, 3H, - C(O)CH3); 13C NMR (150 MHz, CDCl3): δ 170.26, 163.58, 162.83, 138.98, 138.77, 138.60, 138.40, 138.09, 138.04, 137.58, 133.97, 131.97, 129.01, 128.79, 128.71, 128.64, 128.62, 128.56, 128.52, 128.38, 128.32, 128.24, 128.12, 128.05, 127.97, 127.94, 127.84, 127.18, 126.26, 123.57, 117.58, 101.76, 101.35, 98.96, 97.63, 79.24, 78.91, 78.56, 78.22, 75.76, 75.62, 75.03, 74.77, 74.44, 73.75, 72.55, 71.83, 69.94, 69.32, 68.64, 68.54, 68.39, 67.16, 55.88, 36.75, 31.70, 21.27; ESI-MS: m/z calcd for C80H81NO18: 1343.5346; found 1366.5369 (M + Na)+.
Figure imgf000215_0001
[00518] Ally-O-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3)-2,4-O-di- benzyl-β-D- mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranoside (S20f): A mixture of compound S20e (0.630 g, 0.468 mmol) and activated 4 Å molecular sieves in 20 mL CH2Cl2 was stirred for 1 h at rt. The reaction mixture was cooled to -78 oC, triethyl silane (148 µL, 0.946 mmol) followed by dichlorophenyl borane (146 µL, 1.18mmol) was added and stirred for 1 h. The reaction was quenched by Et3N, methanol, filtered through Celite and concentrated in vacuo. The residue was co-distilled with methanol 2-3 times before being purified by flash column chromatography (0%→ 10% EA in toluene) to give alcohol S20f (0.460 g, 73%). TLC: (ethyl acetate: toluene = 2/8, v/v): Rf= 0.42; 1H NMR (600 MHz, CDCl3): δ 7.73-7.57 (m, 4H, Ar-H), 7.50-7.08 (m, 31H, Ar- H), 6.83-6.81 (m, 4H, Ar-H), 5.76-5.69 (m, 1H, Allyl), 5.44 (t, J = 3.0 Hz, 1H), 5.13 (s, 1H, H-1c), 5.12 (s, 1H), 5.08 (d, J = 7.8Hz, 1H, H- 1a), 5.01 (d, J = 11Hz, 1H), 4.93 (d, J = 11.0 Hz, 1H), 4.87 (d, J = 8.6 Hz, 1H), 4.83 (d, J = 8.0 Hz, 1H), 4.76 (d, J = 12.0 Hz, 1H), 4.69 (d, J = 11.0 Hz, 1H), 4.62 (t, J = 8.6 Hz, 1H), 4.57 (t, J = 7.8 Hz, 2H), 4.50 (d, J = 10.8 Hz, 1H), 4.44 (d, J = 2.5 Hz, 1H), 4.42 (s, 1H), 4.40 (d, J = 8.0 Hz, 1H), 4.35 (d, J = 12.0 Hz, 1H), 4.22-4.181 (m, 3H), 4.00-3.99 (m, 2H), 4.90-3.91 (s, 1H), 3.83-3.82 (m, 1H), 3.83 (d, J = 2.4 Hz, 1H), 3.77-3.78 (m, 2H), 3.64-3.54 (m, 6H), 3.41-3.39 (m, 2H), 3.19-3.18 (m, 1H), 2.08 (s, 3H); 13C NMR (150 MHz, CDCl3): δ170.34, 138.90, 138.77, 138.73, 138.36, 138.14, 138.07, 138.03, 135.91, 134.50, 134.03, 133.86, 132.97, 131.94, 131.40, 129.31, 128.86, 128.68, 128.66, 128.61, 128.57, 128.50, 128.45, 128.38, 128.26, 128.20, 128.12, 128.11, 128.03, 127.97, 127.94, 127.79, 127.76, 127.72, 127.47, 127.35, 123.50, 117.59, 101.04, 99.89, 97.61, 80.92, 78.64, 78.48, 78.41, 78.21, 75.93, 75.26, 75.20, 75.19, 75.16, 74.82, 74.59, 74.52, 73.78, 73.75, 72.61, 72.11, 69.91, 69.50, 68.99, 68.43, 62.25, 55.86, 21.29; ESI-MS: m/z calcd for C80H83NO18: 1345.5502; found 1368.5527 (M + Na)+.
Figure imgf000216_0001
[00519] Allyl-O-di-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3),(1→6)-2,4- O-di- benzyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D- glucopyranoside (S20g): A mixture of donor 1 (0.429 g, 0.690 mmol), acceptor S20f (0.460 g, 0.345 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at rt for 30 minutes. The reaction was cooled to -20 oC, boron trifluoride ethyl etherate (19 µL, 0.173 mmol) was then added slowly and the resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 20% EA in hexane) to afford S57 (0.380 g, 65%) as colorless foam. TLC: (ethyl acetate: hexane = 3/7, v/v): Rf = 0.56; 1H NMR (600 MHz, CDCl3):δ 7.60-7.29 (m, 4H, Ar-H), 7.28- 7.08 (m, 37H, AR-H), 7.07-7.08 (m, 8H, Ar-H), 7.07-6.93 (d, J = 8.0 Hz, 1H, Ar-H), 6.82- 6.59 (m, 3H, Ar-H), 5.61-5.59 (m, 1H, Allyl), 5.43 (d, J = 6.0 Hz, 1H, H-2c), 5.31 (d, J = 6.0 Hz, 1H, H-2d), 5.10 (d, J = 3.0 Hz, 1H, H- 1c), 5.06 (d, J = 8.0 Hz, 1H, H-1a), 4.99 (d, J = 10.0 Hz, 1H), 4.85 (d, J = 8.0 Hz, 1H), 4.83 (s, 1H, H-1d), 4.67 (d, J = 8.0 Hz, 1H), 4.64-4.62 (q, 4H), 4.56 (d, J = 3.0 Hz, 1H, H-1b), 4.55-4.45 (m, 8H), 4.45-4.39 (m, 9H), 4.38 (d, J = 10.0 Hz, 1H), 4.21 (d, J = 9.0 Hz, 1H), 4.19-4.10 (m, 2H), 4.08-3.70 (m, 10H), 3.69-3.49 (m, 7H), 3.39 (d, J = 9.1 Hz, 1H), 3.19 (d, J = 9.1 Hz, 1H), 2.07 (s, 3H, -C(O)CH3), 1.82 (s, 3H, - C(O)CH3); 13C NMR (150 MHz, CDCl3): δ 170.31, 170.11, 163.43, 139.07, 138.93, 138.83, 138.80, 138.65, 138.35, 138.32, 138.21, 138.09, 134.08, 133.77, 132.00, 128.87, 128.76, 128.66, 128.56, 128.43, 128.37, 128.16, 127.99, 127.91, 127.82, 127.73, 127.13, 123.46, 117.45, 102.07, 99.92, 99.74, 98.62, 97.55, 81.40, 79.81, 78.31, 78.23, 76.84, 75.87, 75.77, 75.66, 74.87, 74.65, 74.44, 74.38, 31.21, 21.29, 21.23; ESI-MS: m/z calcd for
C109H113NO24: 1820.7578; found 1843.7676 (M + Na)+.
Figure imgf000217_0001
[00520] Di-(2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3),(1→6)-2,4-O-di- benzyl-β-D- mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-gluco- pyranosyl trichloroacetimidate (S20h): To a solution of S20g (0.2 g, 0.109 mmol) in 10 mL CH2Cl2:MeOH (1/1) was added PdCl2 (20 mg) and stirred at room temperature for 6 h until TLC (ethyl acetate: toluene, 2/8) indicated formation of a product with consumption of the starting material. The reaction mixture was then concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford alcohol (0.140 g, 60%) as colorless foam. To a solution of alcohol (0.150 g, 0.084 mmol) in CH2Cl2 (10 mL) was added trichloroacetamidate (33 µL, 0.336 mmol) followed by DBU (12 µL, 0.033 mmol) at 0 oC and stirred at rt for 8 h. The reaction was quenched with Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S20h (0.121 g, 67%) as colorless oil. TLC: (ethyl acetate: toluene = 2/8, v/v): Rf = 0.47; 1H NMR (600 MHz, CDCl3): δ 8.51 (s, 1H, C=NH), 7.53-7.42 (m, 4H, Ar-H), 7.40-7.00 (m, 49H, Ar-H), 6.58 (d, J = 6.6 Hz, 2H, Ar-H), 6.52-6.50 (m, 3H, Ar-H), 5.43 (s, 1H, H-1a), 5.32 (s, 1H, H-1c), 5.03 (s, 1H), 5.01 (t, J = 7.8 Hz, 1H), 4.90-4.78 (m, 6H), 4.67-4.45 (m, 7H), 4.43-4.30 (m, 9H), 4.28-4.20 (m, 2H), 4.10 (t, J = 7.8 Hz, 1H), 3.39-3.42 (m, 18H), 3.19 (d, J = 9.3 Hz, 1H), 2.09 (s, 3H, - C(O)CH3), 1.83 (s, 3H, - C(O)CH3).
Figure imgf000218_0001
[00521] 5-Azidopentyl-O-2,3,4-tri-O-benzyl-α-L-fucopyranosyl-(1→6)-3-O-benzyl-2-deoxy- 2- phthalimido-β-D-glucopyranoside (S20k): A mixture of CuBr2 (0.450 g, 2.01 mmol), Bu4NBr (0.655 g, 2.03 mmol) and activated 4 Å molecular sieves in 10 mL of CH2Cl2 : DMF (2/1) was stirred and cooled over an ice water bath. A solution of donor S20i (0.5 g, 0.925 mmol) and acceptor S20j (0.450 g, 0.882 mmol) in CH2Cl2 (10 mL) was added drop wise and the resulting reaction mixture was stirred at rt for overnight. TLC (ethyl acetate: hexane, 4/6) indicated formation of a product with consumption of the starting material. The reaction was quenched with aq. NaHCO3, diluted with ethyl acetate (50 mL) and filtered through Celite. The filtrate was washed with aq.NaHCO3, brine (50 mL), dried over sodium sulfate. The organic layer was concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 30% EA in hexane) to afford S20k (0.604 g, 76%) as colorless oil. TLC: (ethyl acetate: hexane = 4/6, v/v): Rf = 0.47; 1H NMR (600 MHz, CDCl3): δ 7.80-7.64 (m, 4H, Ar-H), 7.41-7.23 (m, 15H, Ar- H), 7.00-6.98 (m, 2H, Ar-H), 6.90-6.87 (m, 3H, Ar-H), 5.06 (d, J = 8.4 Hz, 1H, H-1a), 4.96 (d, J = 11.4 Hz, 1H), 4.86 (d, J = 11.4 Hz, 1H), 4.82-4.72 (m, 4H), 4.67 (d, J = 12.0 Hz, 1H), 4.64 (d, J = 12.0 Hz, 1H), 4.48 (d, J = 12.6 Hz, 1H), 4.16-4.13 (m, 1H), 4.08-4.05 (m, 2H), 3.39-3.95 (m, 2H), 3.90-3.83 (m, 3H), 3.78 (m, 1H), 3.73-3.69 (m, 2H), 3.56-3.53 (m, 1H), 3.35-3.21 (m, 1H), 2.00-2.03 (m, 2H, -CCH2C-, linker), 1.38-1.30 (m, 4H, -CCH2C-, linker), 1.12 (d, J = 8.4 Hz, 3H, Me of Fucose), 1.00-0.96 (m, 2H, -CCH2C-, linker); 13C NMR (150, MHz, CDCl3): δ 138.83, 138.77, 138.36, 134.13, 128.90, 128.77, 128.67, 128.60, 128.52, 128.31, 128.26, 128.17, 127.93, 127.88, 127.52, 123.64, 98.81, 98.59, 79.60, 78.07, 77.77, 76.67, 75.22, 74.54, 74.51, 74.24, 73.35, 73.20, 69.37, 68.79, 67.15, 55.88, 51.39, 29.00, 28.58, 23.30, 16.89; ESI-MS: m/z calcd for C53H58N4O11: 926.3994; found 949.3998 (M + Na)+.
Figure imgf000219_0001
[00522] 5-Azidopentyl-O-2-O-acetyl-3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→6)-(2-O- acetyl- 3,4,6-tri-O-benzyl-α-D-mannopyranosyl-(1→3))-2,4-di-O-benzyl-β-mannopyranosyl- (1→4)-O-3,6-di-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl-(1→4)-(2,3,4-tri-O- benzyl-α-L-fuco pyranosyl-(1→6))-3-O-benzyl-2-deoxy-2-phthalimido-β-D-glucopyranoside (S20l): A mixture of donor S20h (0.050 g, 0.025 mmol), acceptor S20k (0.028 g, 0.031 mmol) and activated 4 Å molecular sieves in dry CH2Cl2 (10 mL) was stirred at rt for 30 minutes. The reaction was cooled to -70 oC, boron trifluoride ethyl etherate (0.725 µL, 0.0062 mmol) was then added slowly and the resulting reaction mixture was stirred for 2 h. The reaction was quenched by adding Et3N, diluted with CH2Cl2, filtered through Celite and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 20% EA in hexane) to afford S20l (0.027 g, 45%) as a white foam. TLC: (ethyl acetate : hexane = 3/7, v/v): Rf = 0.50; 1H NMR (600 MHz, CDCl3): δ 7.83-7.62 (m, 7H, Ar-H), 7.49-7.30 (m, 8H, Ar-H), 7.30-7.10 (m, 47H, Ar- H), 7.09-7.03 (m, 10H, AR-H), 7.03-6.99 (m, 1H, Ar-H), 6.93 (d, J = 8.9 Hz, 2H, AR-H), 6.79-6.63 (m, 6H, AR-H), 6.55 (t, J = 7.8 Hz, 2H, H-2d,d'), 5.40 (s, 1H, H-1d), 5.29-5.29 (m, 1H), 5.09 (d, J = 1.3 Hz, 1H, H1d’), 4.88-4.76 (m, 13H), 4.67-4.65 (m, 2H), 4.58-5.48 (m, 9H), 4.42-4.40 (m, 3H), 4.36-4.30 (m, 5H), 4.20- 4.10 (m, 5H), 4.05-4.00 (m, 2H), 3.92-3.80 (m, 7H), 3.79-3.60 (m, 7H), 3.62-3.41 (m, 10H), 3.25(dd, J = 3.2, 8.2 Hz, 1H), 3.18-3.17 (m, 2H), 2.85-2.79 (m, 2H), 2.06 (s, 3H, -C(O)CH3), 1.76 (s, 3H, -C(O)CH3, 1.42-1.34 (m, 4H, -CCH2C-, linker), 1.03-0.99 (m, 5H, -CCH2C-, linker and CH3 of Fucose); 13C NMR (150 MHz, CDCl3): δ 170.30, 169.91, 168.15, 167.76, 139.16, 138.99, 138.88, 138.82, 138.77, 138.54, 138.28, 138.21, 138.10, 138.08, 138.05, 133.86, 132.02, 131.72, 128.80, 128.62, 128.60, 128.57, 128.55, 128.33, 128.23, 128.40, 127.98, 127.92, 127.70, 127.55, 127.26, 127.06, 123.33, 101.97, 99.62, 98.41, 97.95, 97.09, 97.05, 81.42, 79.71, 78.36, 74.98, 74.75, 74.68, 73.65, 72.57, 72.51, 72.03, 71.38, 68.93, 68.86, 68.12, 66.63, 66.12, 56.76, 56.01, 51.26, 28.82, 28.56, 23.20, 21.23, 20.91; ESI-MS: m/z calcd for C159H165N5O34: 2689.1261; found 2712.1338 (M + Na)+.
Figure imgf000220_0001
[00523] 5-Aminopentyl-di-(α-D-mannopyranosyl)-(1→3),(1→6)-β-D-mannopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-(α-L-fucopyranosyl-(1→6)-2- acetamido-2- deoxy-β-D-glucopyranoside (G3): Compound S20h (0.030 g, 0.011 mmol) was deprotected by following general procedure 2 (method 1) to obtain the title compound G3 (0.007 g, 22%) as a white powder. 1H NMR (600 MHz, D2O): δ 5.09 (s, 1H, H-1d), 4.91 (s, 1H, H-1d'), 4.89 (d, J = 3.2 Hz, 1H, H-1e), 4.78 (s, 1H, H-1c), 4.65 (d, J = 7.8 HZ, 1H, H-1a), 4.49 (d, J = 7.8 Hz, 1H, H- 1b), 4.25 (s, 1H), 4.15-4.10 (m, 1H), 4.05 (s, 1H), 3.95 (s, 1H), 3.95-3.80 (m, 8H), 3.80-3.50 (m, 23H), 3.00 (m, 2H), 2.10 (s, 3H, -C(O)CH3), 2.09 (s, 3H, - C(O)CH3, 1.67-1.60 (m, 2H, -CCH2C-), 1.60-1.57 (m, 2H, -CCH2C-), 1.41-1.37 (m, 2H, - CCH2C-), 1.25 (d, J = 7.8 Hz, 3H, -CH3 of Fucose); 13C NMR (150 MHz, D2O): δ 174.67, 174.39, 170.97, 102.51, 101.10, 101.04, 100.38, 99.60, 99.39, 80.46, 79.72, 78.60, 74.33, 74.15, 73.42, 72.65, 72.30, 71.95, 71.85, 70.29, 70.12, 70.00, 69.97, 69.85, 69.45, 68.15, 66.77, 66.14, 65.85, 65.80, 61.11, 60.92, 59.97, 55.05, 54.86, 46.66, 39.28, 38.61, 28.05, 26.36, 22.27, 22.15, 21.08, 21.50, 15.37, 15.34; ESI-MS: m/z calcd for C45H80N3O30; 1141.4821; found 1142.4827 (M + H)+.
Figure imgf000221_0001
[00524] 5-Aminopentyl-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2)-α-D-mannopyranosyl]-(1→3),(1→6)-β-D-mannopyranosyl-(1→4)- 2-acetamido-2- deoxy-β-D-glucopyranosyl-(1→4)-(α-L-fucopyranosyl-(1→6)-2-acetamido- 2-deoxy-β-D- glucopyranoside (G19): Sialylated biantennary with core fucose glycan G19 was prepared by using reported procedure11,12. 1H NMR (600 MHz, D2O): δ 4.90 (s, 1H, H-1d), 4.72 (s, 1H, H- 1d'), 4.66 (d, J = 3.6 Hz, 1H, H-1c), 4.56 (s, 1H), 4.43 (d, J = 7.2 Hz, 1H, H-1b), 4.37 (d, J = 7.2 Hz, 2H, H-1e,e'), 4.25 (d, J = 7.8 Hz, 1H, H-1a), 4.21 (d, J = 7.8 Hz, 2H, H-1f), 4.04 (s, 1H), 3.97 (s, 1H), 3.90 (t, J = 10.1 Hz, 2H), 3.76-3.25 (m, 65H), 2.74 (t, J = 7.8 Hz, 2H, linker), 2.43 (dd, J = 3.8 & 7.2 Hz, 1H, H-3equi. g, g'), 1.87 (s, 3H), 1.84 (s, 3H, -C(O)CH3), 1.83 (s, 3H, -C(O)CH3), 1.80 (s, 6H, -C(O)CH3), 1.51 (t, J = 12 H, 2H, H-3axial g,g'), 1.46-1.41 (m, 2H), 1.37-1.34 (m, 2H), 1.18-1.15 (m, 2H), 1.00 (d, J = 6.6 Hz, 3H, -CH3 of Fucose); 13C NMR (150 MHz, D2O): δ 174.5, 174.3, 174.1, 173.3, 103.3, 100.9, 100.7, 100.2, 99.7, 99.6, 99.3, 99.1, 98.9, 96.5, 80.2, 79.5, 77.8, 75.9, 75.6, 74.0, 73.3, 73.2, 73.1, 72.4, 72.2, 71.8, 71.7, 71.3, 70.3, 69.9, 69.7, 69.3, 69.1, 68.0, 67.9, 67.0, 66.9, 66.5, 65.7, 65.4, 63.0, 62.2, 61.4, 61.3, 59.8, 59.4, 54.7, 54.4, 54.2, 51.5, 39.7, 38.9, 27.7, 26.1, 22.1, 22.0, 22.0, 21.8, 21.7, 15.1 ; ESI-MS: m/z calcd for C95H159N7O66; 2451.9121; found 1226.4513 (M - H)2-.
[00525] Synthesis of glycans with phosphonic acid tails S
[00526] General procedure: To a solution of sugars with amine tail (3-5 µmol) in DMF (400 µL) was added linker [2(2(2(bis(benzyloxy)phosphoryl)ethoxyethoxy)ethyl(2,5- dioxopyrrolidin-1- yl)carbonate] (15-25 µmol), and the resulting reaction mixture was stirred at rt for 5 h. DMF was removed by using high vacuum and the product was purified by using Bio-Gel P-2 chromatography (eluent H2O). The solid was dissolved in 2 mL of H2O, added Pd(OH)2 (50% by weight) and hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO- RAD) column chromatography using water as eluent. The product was the lypholysed to obtain the desired sugar with phosphonic acid tail as white color powder.
Figure imgf000222_0001
[00527] Scheme S21 | Preparation of sugars with phosphonic acid linker. i, (1) Linker, DMF, RT, 5 h; (2) Pd(OH)2, H2O, H2, RT, overnight.
Figure imgf000223_0001
[00528] β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2- acetamido-2-deoxy-β-D-glucopyranoside (I): Compound S23 (3.5 mg, 5.4 µmol) was modified by above general procedure to afford compound I (2.2 mg, 61%), as white solid. TLC (MeOH: EA:AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 4.60 (d, J = 8.4 Hz, 1H), 4.48 (d, J = 7.8 Hz, 1H), 4.19 (s, 2H), 4.05 (d, J = 3.2 Hz, 1H), 3.93-3.49 (m, 33H), 1.75 (t, J = 7.8 Hz, 2H), 2.06 (s, 3H), 1.95 (s, 3H), 1.95-1.92 (m, 2H), 1.58-1.54 (m, 2H), 1.50-1.47 (m, 2H), 1.33-1.30 (m, 2H). HRMS (MALDI-TOF): m/z calcd for
C34H59N3O23P; 908.3067 found 954.3099 (M + 2Na)+.
Figure imgf000223_0002
[00529] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-α-D-manno- pyranosyl(1→3)-α- D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2- deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (II): Glycan G2 (4 mg, 2.3 µmol) was modified by above general procedure to afford compound II (3.2 mg, 71%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.01 (s, 1H), 4.83 (s, 1H), 4.51 (d, J = 6.1 Hz, 1H), 4.40 (d, J = 6.2 Hz, 1H), 4.17 (s, 1H), 4.11 (s, 2H), 3.98 (s, 1H), 3.88-3.39 (m, 52H), 3.03 (t, J = 7.8 Hz, 2H), 1.99 (s, 3H), 1.95 (s, 3H), 1.95-1.91 (m, 2H), 1.50-1.45 (m, 2H), 1.42-1.38 (m, 2H), 1.26-1.22 (m, 2H). HRMS (MALDI-TOF) Negative mode: m/z calcd for C58H102N3O43P; 1234.4484 found 1278.5001 (M + 2Na - 2H)-.
Figure imgf000224_0001
[00530] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-α-D-manno- pyranosyl(1→3)-α- D-mannopyranosyl]-(1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2- deoxy-β-D- glucopyranosyl-(1→4)-)-(α-L-fucopyranosyl-(1→6)-2-acetamido-2-deoxy-β-D- glucopyranoside) (III): Glycan G3 (1.2 mg, 1.0 µmol) was modified by above general procedure to afford compound III (1.0 mg, 91%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.09 (s, 1H), 4.90 (s, 1H), 4.88 (d, J = 7.4 Hz, 1H), 4.66 (d, J = 7.5 Hz, 1H), 4.48 (d, J = 7.2 Hz, 1H), 4.25 (s, 1H), 4.19 (s, 2H), 4.12- 4.10 (m, 1H), 4.06 (s, 1H), 3.95 (s, 1H), 3.92-3.84 (m, 10H), 3.79-3.69 (m, 31H), 3.11-3.09 (m, 2H), 2.08 (s, 3H), 2.02 (s, 3H), 1.99-1.93 (m, 2H), 1.58-1.53 (m, 2H), 1.49-1.47 (m, 2H), 1.34-1.30 (m, 2H), 1.22 (d, 3H). HRMS (MALDI-TOF): m/z calcd for C34H59N3O23P; 1381.5709.3067 found 1450.5709 (M + 3Na)+.
Figure imgf000224_0002
[00531] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-α-D-manno- pyranosyl(1→3),[di- (α-D-mannopyranosyl)-(1→3),(1→6)-α-D-mannopyranosyl]-(1→6)-β- D-mannopyranosyl- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido- 2-deoxy-β-D- glucopyranoside (IV): Glycan G4 (4 mg, 3.1 µmol) was modified by above general procedure to afford compound IV (3.7 mg, 78%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.10 (d, J = 9.6 Hz, 2H), 4.93 (s, 1H), 4.70 (s, 1H), 4.57 (d, J = 7.2 Hz, 1H), 4.48 (d, J = 7.8 Hz, 1H), 4.24 (d, J = 3.2 Hz, 2H), 4.19-4.13 (m, 4H), 4.06-4.04 (m, 3H), 3.95-3.40 (m, 45H), 3.38-3.37 (m, 1H), 2.10 (t, J = 7.8 Hz, 2H), 2.07 (s, 6H), 2.02 (s, 6H), 1.98-1.93 (m, 2H), 1.58-1.47 (m, 2H), 1.34-1.29 (m, 2H), 1.27-1.25 (m, 2H); HRMS (MALDI-TOF): m/z calcd for C58H102N3O43P; 1560.3985 found 1607.0452 (M + 2Na + H)+.
Figure imgf000225_0001
[00532] (Phosphonate-tri-(ethylene glycol)-carbonyl-amino)-pentyl-α-D-mannopyranosyl- (1→2)-α- D-mannopyranosyl-(1→2)-α-D-manno- pyranosyl-(1→3)-β-D-manno- pyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside (V): Glycan G5 (5 mg, 4.4 µmol) was modified by above general procedure to afford compound V (3.5 mg, 58%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.34 (s, 1H), 5.29 (s, 1H), 5.03 (s, 1H), 4.58 (d, J = 7.8 Hz, 1H), 4.47 (d, J = 7.8 Hz, 1H), 4.20 (bs, 3H), 4.09-4.05 (m, 3H), 3.90-3.20 (m, 41H), 3.10 (t, J = 7.8 Hz, 2H), 2.05 (s, 3H), 2.01 (s, 3H), 2.00-1.92 (m, 2H), 1.56-1.53 (m, 2H), 1.49-1.46 (m, 2H), 1.33-1.30 (m, 2H); HRMS (MALDI-TOF): m/z calcd for
C52H92N3O38P; 1398.2579 found 1444.5470 (M + 2Na)+.
Figure imgf000226_0001
[00533] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-α-D-mannopyranosyl- (1→2)-α- D-mannopyranosyl-(1→2)-α-D-manno- pyranosyl-(1→3)-{α-D-mannopyranosyl- (1→2)-α- D-mannopyranosyl-(1→3)-[α-D-manno- pyranosyl-(1→2)-α-D-mannopyranosyl- (1→6)]-α- D-mannopyranosyl-(1→6)}-β-D-manno- pyranosyl-(1→4)-2-acetamido-2-deoxy- β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (VI): Glycan G6 (4 mg, 2.0 µmol) was modified by above general procesure to afford compound VI (3.7 mg, 66%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.53 (s, 1H), 5.39 (d, J = 10.2 Hz, 1H), 5.26 (d, J = 9.8 Hz, 1H), 5.23 (s, 1H), 5.16 (d, J = 4.8 Hz, 1H), 5.08-5.05 (m, 5H), 4.60 (d, J = 7.8 Hz, 1H), 4.50 (d, J = 7.8 Hz, 1H), 2.08 (s, 3H), 2.02 (s, 3H), 1.38-1.03 (m, 2H), 1.58-1.56 (m, 2H), 1.52-1.48 (m, 2H), 1.35-1.32 (m, 2H); HRMS (MALDI- TOF): m/z calcd for C82H142N3O63P; 2209.0310 found 2257.0812 (M + 2Na)+.
Figure imgf000226_0002
[00534] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-β-D-galactopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl -(1→2)-α-D-mannopyranosyl]-(1→3)-β- D- mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido- 2- deoxy-β-D-glucopyranoside (VII): Glycan G9 (6.0 mg, 5.1 µmol) was modified by above general procedure to afford compound VII (3.5 mg, 50%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.03 (d, J = 8.4 Hz, 2H), 4.58 (d, J = 7.2 Hz, 1H), 4.48 (d, J = 7.2 Hz, 1H), 4.45 (d, J = 7.8 Hz, 1H), 4.26 (dd, J = 3.0 & 9.2 Hz, 2H), 4.19 (bs, 2H), 4.00-3.38 (m, 48H), 3.11 (t, J = 7.8 Hz, 2H), 2.06 (s, 3H), 2.05 (s, 3H), 2.02 (s, 3H), 1.99-1.93 (m, 2H), 1.56-1.54 (m, 2H), 1.50-1.48 (m, 2H), 1.31-1.27 (m, 2H); HRMS (MALDI- TOF): m/z calcd for C54H92N4O38P; 1435.4917 found 1481.5069 (M + 2Na)+.
Figure imgf000227_0001
[00535] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-β-D-galactopyranosyl- (1→4)-[2- acetamido-2-deoxy-β-D-gluco-pyranosyl-(1→2)-α-D-mannopyranosyl-(1→3),[di- (α-D- mannopyranosyl)-(1→3),(1→6)-α-D-manno-pyranosyl](1→6)-β-D-mannopyranosyl- (1→4)- 2-acetamido-2-deoxy-β-D-gluco-pyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside (VIII): Glycan G12 (5.0 mg, 3.0 µmol) was modified by above general procedure to afford compound VIII (3.1 mg, 54%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.11 (s, 2H), 5.02 (d, J = 7.8Hz, 2H), 4.68 (d, J = 3.2 Hz, 2H), 4.48 (d, J = 7.2 Hz, 1H), 4.45 (d, J = 7.2 Hz, 1H), 4.27 (s, 2H), 4.22 (s, 2H), 4.15 (s, 1H), 4.08 (s, 2H), 4.00-3.30 (m, 60H), 3.10 (t, J = 7.8 Hz, 2H), 2.08 (s, 3H), 2.05 (s, 3H), 2.02 (s, 3H), 1.93-1.87 (m, 2H), 1.56-1.54 (m, 2H), 1.51-1.47 (m, 2H), 1.33- 1.30 (m, 2H); HRMS (MALDI-TOF): m/z calcd for C72H122N4O53P; 1921.6502 found 1967.6622 (M + 2Na)+.
Figure imgf000228_0001
[00536] Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-[5-Acetamido-3,5- dideoxy-D- glycero-α-D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→3)-β- D- mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-gluco-pyranosyl-(1→4)-2-acetamido- 2- deoxy-β-D-glucopyranoside (IX): Glycan G10 (5.0 mg, 2.5 µmol) was modified by above general procedure to afford compound IX (3.8 mg, 63%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.08 (d, J = 8.4 Hz, 2H), 4.93 (s, 1H), 4.62 (d, J = 7.2 Hz, 1H), 4.51 (d, J = 7.8 Hz, 1H), 4.45 (d, J = 7.8 Hz, 1H), 4.30 (d, J = 3.2 Hz, 1H), 4.28 (s, 1H), 4.22 (s, 2H), 4.02-3.30 (m, 53H), 3.13 (t, J = 7.8 Hz, 2H), 2.68 (dd, J = 3.2, 7.8 Hz, 1H), 2.09 (s, 6H), 2.05 (s, 6H), 2.01-1.93 (m, 2H), 1.74 (t, J = 12.1 Hz, 1H), 1.60-1.57 (m, 2H), 1.54-1.51 (m, 2H), 1.35-1.32 (m, 2H); HRMS (MALDI-TOF): m/z calcd for C65H109N5O46P; 1726.5871 found 1772.5817 (M + 2Na)+.
Figure imgf000228_0002
[00537] (Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-5-Acetamido-3,5- dideoxy-D- glycero-α-D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl- (1→4)-[2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3),[di- (α-D- mannopyranosyl)-(1→3),(1→6)-α-D-manno-pyranosyl](1→6)-β-D-mannopyranosyl- (1→4)- 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranoside (X): Glycan G13 (4.0 mg, 2.3 µmol) was modified by above general procedure to afford compound X (3.2 mg, 71%), as white solid. TLC (MeOH: EA: AcOH: H2O, 7/1/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.08 (d, J = 10.2 Hz, 1H), 5.03 (s, 1H), 4.94 (s, 2H), 4.91 (s, 1H), 4.62 (s, 1H), 4.51 (d, J = 6.6 Hz, 1H), 4.46 (d, J = 7.8 Hz, 1H), 4.30 (s, 2H), 4.25 (s, 2H), 4.17 (s, 1H), 4.06 (s, 1H), 4.00-3.20 (m, 70H), 2.70 (dd, J = 3.2, 7.8 Hz, 1H), 2.11 (s, 6H), 2.05 (s, 6H), 2.03-1.97 (m, 2H), 1.14 (t, J = 12.6 Hz, 1H), 1.58-1.51 (m, 4H), 1.36-1.31 (m, 2H). HRMS (MALDI-TOF): m/z calcd for C83H144N5O61P; 1102.2301 found 1148.2946 (M + 2Na)2-.
Figure imgf000229_0001
[00538] Phosphonate-tri-(ethyleneglycol)-carbonyl-amino)-pentyl-di-[5-Acetamido-3,5- dideoxy-D- glycero-α-D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl- (1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D-mannopyranosyl]- (1→3),(1→6)-β-D- mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranosyl- (1→4)-2-acetamido-2- deoxy-β-D-glucopyranoside (XI): Glycan G16 (3.5 mg, 1.5 µmol) was modified by above general procedure to afford compound XI (2.6 mg, 69%) as a white solid. TLC (MeOH: AcOH: H2O, 8/1/1, v/v). 1H NMR (600 MHz, D2O): δ 5.05 (d, J = 8.4 Hz, 1H), 4.63 (d, J = 6.6 Hz, 1H), 4.51 (s, 1H), 4.46 (t, J = 7.8 Hz, 2H), 4.32 (s, 1H), 4.29 (s, 2H), 4.22 (s, 2H), 4.09-3.48 (m, 79H), 3.13 (t, J = 7.8 Hz, 2H), 2.74-2.68 (m, 2H), 2.10 (s, 9H), 2.05 (s, 9H), 2.12-2.00 (m, 2H), 1.76-1.73 (m, 2H), 1.58-1.55 (m, 2H), 1.51-1.50 (m, 2H), 1.35-1.29 (m, 2H); HRMS (MALDI-TOF negative mode): m/z calcd for
C96H162N7O69P; 2547.9096 found 1294.9685 (M + Na)2-.
[00539] Chemo-enzymatic synthesis of D1 and D2/D3 arm modules S
[00540] Our chemo-enzymatic strategy commensed with preparation of acceptor substrates 16-20. As depicted in scheme S22, mannosyl acceptor S22b was glycosylated with donor S22a in the presence of NIS/TfOH to afford the disaccharide S22c in 60% yield.
Benzyledine ring of S22c was opened both at 4-OH, S22d or 6-OH, S22g under diffirent reaction conditions. Donor S22e was installed separately at 4-O and 6-O positions of S22d and S22g respectively. Finally, global deprotection of intermidiates S22c, S22f and S22h was performed. In case of compounds S22j and S22l, the GlcNAc residues at Man 4 and 6-O positions were diffirenciated from 2-O GlcNAc through acetylation of 4-OH, for preparation of assymetric modules.
Figure imgf000230_0001
[00541] Scheme S22 | Preparation of acceptor substrates. i, NIS, TfOH, CH2Cl2, -50 oC, 3 h; ii, Triethyl silane, TFA, 4 Å MS,CH2Cl2, 0 oC, 2 h, 58%; iii, BH3.THF, Bu2BOTf, CH2Cl2, 4 Å MS, -10 oC, 1 h, 71%; iv, (1) NH2CH2CH2NH2, nBuOH, 100 oC; (2) Ac2O, pyridine, 0 oC to RT; (3) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2;
Figure imgf000231_0001
[00542] p-methoxyphenyl-O-[4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- gluco- pyranosyl-(1→2)-O-4,6-O-benzylidene-3-O-benzyl-α-D-mannopyranoside (S22c): Activated 4Å molecular sieves (1 g) were added to a solution of acceptor S22b (0.250 g, 0.536 mmol) and donor S22a (0.410 g, 0.643 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at rt then cooled to -50 oC. NIS (0.241 g, 1.07 mmol) and TfOH (11.8 µ L, 0.134 mmol) were added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (ethyl acetate: toluene, 2/8) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 10% EA in toluene) to afford S22c (0.403 g, 76%) as a white foam. TLC (ethyl acetate: toluene = 2/8, v/v); Rf = 0.49; 1H NMR (400 MHz, CDCl3): δ 7.69-3.56 (m, 4H), 7.36-7.22 (m, 15H), 7.20-6.96 (m, 5H), 6.53 (d, J = 8.4 Hz, 2H), 6.50 (d, J = 8.2 Hz, 2H), 5.41 (s, 1H), 5.24 (d, J = 7.8 Hz, 1H), 5.10 (t, 1H), 4.93 (s, 1H), 4.73-4.43 (m, 10H), 4.00-3.20 (m, 5H), 1.98 (s, 3H) ; 13C NMR (150 MHz, CHCl3): δ 169.2, 152.3, 135.1, 134.9, 133.9, 128.7, 128.6, 128.4, 128.1, 128.1, 128.0, 127.7, 127.6, 127.5, 117.8, 114.7, 97.1, 96.3,74.0, 73.9, 73.1, 72.9, 72.8, 72.8, 72.5, 72.2, 71.4, 65.7, 55.4, 54.2, 22.5; ESI-MS: m/z calcd for C57H55NO14; 977.3623 found 1000.3490 (M + Na)+.
Figure imgf000232_0001
[00543] p-methoxyphenyl-O-[4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- gluco-pyranosyl-(1→2)-O-3,6-O-dibenzyl-α-D-mannopyranoside (S22d): To a solution of S22c (1.01 g, 1.02 mmol) in anhydrous CH2Cl2 (10 mL) was added triethyl silane (1.63 mL, 10.2 mmol) followed by trifluroacetic acid (0.758 mL, 10.2 mmol) at 0 oC. The resulting reaction mixture was stirred for 3 h. After 3 h, TLC (ethyl acetate: toluene, 1.5/8.5 v/v) indicated product formation with consumption of starting material. The reaction mixture was washed with sat. NaHCO3 (2 x 50 mL). The aqueous layer was further extracted with CH2Cl2 (3 x 30 mL), and the combined organic layer were washed with brine solution (100 mL), dried over MgSO4, filtered and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S22d (0.580 g, 65%) as clear oil. TLC (ethyl acetate: toluene = 1.5/8.5, v/v): Rf = 0.35; 1H NMR (400 MHz, CDCl3): δ 7.63-7.35 (m, 4H), 7.30-7.10 (m, 14H), 7.02-6.97 (m, 3H), 6.93-6.86 (m, 3H), 6.72-6.66 (m, 4H), 5.27 (d, J = 8.4 Hz, 1H), 5.11 (t, J = 10.2 Hz, 1H), 5.02 (d,J = 2.8 Hz, 1H), 4.88 (s, 2H), 4.80 (s, 1H), 4.60 (d, J = 10.2 Hz, 2H), 4.58-4.24 (m, 6H), 4.01 (s, 2H), 3.79- 3.74 (m, 2H), 3.72 (s, 3H), 3.64-3.56 (m, 3H), 3.35 (dd, J = 2.8 & 8 Hz, 1H), 2.93 (dd, J = 2.3 & 7.8 Hz, 1H), 1.94 (s, 3H); 13C NMR (150 MHz, CHCl3): δ 150.33, 138.18, 137.98, 133.96, 128.70, 128.65, 128.42, 128.18, 128.12, 128.02, 127.76, 127.62, 127.52, 117.89, 114.71, 97.19, 96.33,74.08, 73.96, 73.10, 72.95, 72.80, 71.86, 70.96, 70.75, 70.48, 67.72, 55.89, 55.69, 21.21; ESI-MS: m/z calcd for C57H57NO14; 979.3779 found 1002.3660 (M + Na)+.
Figure imgf000233_0001
[00544] p-methoxyphenyl-O-4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-gluco pyranosyl-(1→2)-[-O-4,6-O-benzylidene-3-O-benzyl-2-deoxy-2-phthalimido-β-D-gluco pyranosyl-(1→4)]-3,6-O-di-benzyl-α-D-mannopyranoside (S33f): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S22d (0.580 g, 0.590 mmol) and donor S22e (0.525 g, 0.880 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at rt then cooled to -50 oC. NIS (0.265 g, 1.14 mmol) and TfOH (13 µ L, 0.147 mmol) were added slowly, and the resulting reaction mixture was stirred for 2 h. When TLC (ethyl acetate: toluene, 1.5/8.5) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S22f (0.730 g, 85%) as a pale yellow solid. TLC (ethyl acetate: toluene = 1.5/8.5, v/v): Rf =0.60; 1H NMR (400 MHz, CDCl3): δ 7.69- 6.67 (m, 8H), 7.59-7.18 (m, 20H), 6.96-6.75 (m, 10H), 6.57-6.52 (m, 4H), 5.44 (s, 1H), 5.27 (d, J = 8.4 Hz, 1H), 5.21 (d, J = 8.8 Hz, 1H), 5.11 (t, J = 10.7 Hz, 1H), 3.29-3.24 (m, 1H), 4.94 (d,J = 8.4 Hz, 1H), 4.76-4.69 (m, 2H), 4.57 (d, J = 7.8 Hz, 1H), 4.53 (d, J = 7.2 Hz, 1H), 4.45-4.19 (m, 9H), 4.10-4.06 (m, 2H), 3.99-3.94 (m, 2H), 3.63 (s, 3H), 3.56 -3.48 (m, 8H), 3.00 (dd, J = 2.3 and 7.8 Hz, 2H), 1.99 (s, 3H); 13C NMR (150 MHz, CHCl3): δ 169.98, 168.04, 138.94, 138.46, 138.14, 137.96, 133.90, 131.78, 129.24, 128.69, 128.52, 128.34, 128.25, 128.18, 128.08, 127.72, 127.33, 126.38, 123.56, 117.90, 114.47, 101.43.99.38, 83.11, 78.85, 74.79, 74.27, 73.94, 73.76, 72.80, 72.34, 71.43, 70.26, 69.23, 68.90, 66.00, 56.49, 55.85, 55.70, 21.70; ESI-MS: m/z calcd for
C85H80N2O20; 1448.5153 found 1471.5156 (M + Na)+.
Figure imgf000234_0001
[00545] p-methoxyphenyl-O-[4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D- gluco-pyranosyl-(1→2)-O-3,4-O-dibenzyl-α-D-mannopyranoside (S22g): To a mixture of compound S22c (0.800 g, 0.816 mmol) and activated molecular sieves (1 g) in anhydrous CH2Cl2 (10 mL) was added borane. THF complex (0.781 mL of a 1M solution in THF, 8.15 mmol) and Bu2BOTf (0.351 mL of a 1M solution in CH2Cl2, 1.63 mmol) were added at 0°C. The reaction mixture was allowed to stirred at room temperature for 3 h. TLC (acetone: toluene, 1/9) indicated formation of a product with consumption of the starting material. Triethyl amine was added to the reaction mixture followed by slow addition of methanol at 0 °C. When no more hydrogen was produced, the reaction mixture was filtered through Celite, The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S22g (0.500 g, 62%) as clear foam. TLC (acetone: toluene = 2/8, v/v): Rf = 0.41; 1H NMR (400 MHz, CDCl3): δ 7.84-7.55 (m, 4H), 7.40-6.90 (m, 10H), 6.87-6.80 (m, 7H), 6.93-6.86 (m, 3H), 6.72-6.66 (m, 4H), 5.27 (d, J = 8.4 Hz, 1H), 5.11 (t, J = 10.2 Hz, 1H), 5.02 (d,J = 2.8 Hz, 1H), 4.88 (s, 2H), 4.80 (s, 1H), 4.60 (d, J = 10.2 Hz, 2H), 4.58-4.24 (m, 6H), 4.01 (s, 2H), 3.79- 3.74 (m, 2H), 3.72 (s, 3H), 3.64-3.56 (m, 3H), 3.35 (dd, J = 2.8 & 8 Hz, 1H), 2.93 (dd, J = 2.3 & 7.8 Hz, 1H), 1.94 (s, 3H); 13C NMR (150 MHz, CHCl3): δ 154.2, 138.6, 136.5, 133.5, 128.0, 127.5127.4, 128.18, 127.1, 127.0, 126.7, 126.6, 126.5, 117.89, 114.71, 97.19, 96.33,74.08, 73.96, 73.10, 72.9, 72.8, 72.5, 72.6, 71.9, 71.4, 65.7, 56.8, 56.6, 21.9; ESI-MS: m/z calcd for C57H57NO14; 979.2640; found 979.2012.
Figure imgf000235_0001
[00546] p-methoxyphenyl-O-4-O-acetyl-3,6-O-di-benzyl-2-deoxy-2-phthalimido-β-D-gluco pyranosyl-(1→2)-[-O-4,6-O-benzylidene-3-O-benzyl-2-deoxy-2-phthalimido-β-D-gluco pyranosyl-(1→6)]-3,6-O-di-benzyl-α-D-mannopyranoside (S22h): Activated 4 Å molecular sieves (1 g) were added to a solution of acceptor S22g (0.500 g, 0.509 mmol) and donor S22e (0.452 g, 0.763 mmol) in anhydrous CH2Cl2 (10 mL). The reaction mixture was stirred for 1 h at room temperature then cooled to -50 oC. NIS (0.229 g, 1.01 mmol) and TfOH (22 µL, 0.250 mmol) were added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (ethyl acetate: toluene, 1/9) indicated formation of product with consumption of starting material, the reaction was quenched by adding Et3N then filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 50 mL), aqueous Na2S2O3 (2 x 50 mL), and brine (50 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 10% EA in toluene) to afford S22h (0.610 g, 82%) as a pale yellow solid. TLC (ethyl acetate: toluene = 1/9, v/v): 1H NMR (400 MHz, CDCl3): δ 7.75-7.50 (m, 8H), 7.47-7.05 (m, 25H), 7.02-6.82 (m, 10H), 6.66 (d, J = 8.5 Hz, 2H), 6.48 (d, J = 8.6 Hz, 2H), 5.38 (s, 1H), 5.17 (d, J = 8.4 Hz, 1H), 5.21 (t, J = 10.3 Hz, 1H), 4.85 (d, J = 8.6 Hz, 1H), 3.29-3.24 (m, 1H), 4.94 (d, J = 8.4 Hz, 1H), 4.76- 4.69 (m, 2H), 4.57 (d, J = 7.8 Hz, 1H), 4.53 (d, J = 7.2 Hz, 1H), 4.45-4.19 (m, 9H), 4.10-4.06 (m, 2H), 3.99-3.94 (m, 2H), 3.63 (s, 3H), 3.56 - 3.55 (m, 6H), 3.44-3.25 (m, 2H), 3.00 (t, J = 10.3 Hz, 2H), 1.99 (s, 3H); 13C NMR (150 MHz, CHCl3): δ 170.0, 154.9, 150.7, 146.8, 138.6, 137.9, 137.4, 137.1, 136.9, 133.9, 132.7, 129.24, 128.69, 128.52, 128.34, 128.25, 127.9, 127.72, 127.33, 126.38, 123.56, 117.90, 114.47, 101.43.99.38, 83.11, 78.85, 74.79, 74.27, 73.94, 73.76, 72.80, 72.34, 71.43, 70.26, 69.23, 68.90, 66.00, 58.49, 56.8, 56.7, 55.90, 55.8, 21.8; ESI-MS: m/z calcd for C85H80N2O20; 1448.5153 found 1449.5678 (M + H)+.
Figure imgf000236_0001
[00547] p-methoxyphenyl-O-2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→2)-α-D- mannopyranoside (16): Compound S22c (0.105 g, 0.107 mmole) was deprotected by following general procedure 2 (method 1) to get the title compound 16 (0.035 g, 66%) as a white solid. 1H NMR (400 MHz, D2O): δ 7.08 (d, J = 9.6 Hz, 2H), 6.92 (d, J = 9.1 Hz, 2H), 5.43 (s, 1H), 4.60 (d, J = 8.4 Hz, 1H), 4.25 (t, J = 2.3 Hz, 1H), 4.01 (dd, J = 3.2 & 10.1 Hz, 1H), 3.87 (dd, J = 3.1 & 12.2 Hz, 1H), 3.80 (dd, J = 3.0 & 12.8 Hz, 1H), 3.78 (s, 3H), 3.72- 3.67 (m, 3H), 3.61-3.52 (m, 3H), 3.46- 3.40 (m, 2H), 1.99 (s, 3H), 13C NMR (150 MHz, D2O): δ 174.64, 170.85, 154.46, 149.57, 118.60, 114.83, 99.57, 96.50, 76.24, 75.67, 73.35, 73.10, 69.67, 69.28, 66.90, 61.14, 60.40, 55.55, 55.20; ESI-MS: m/z calcd for C21H31NO1; 489.1738 found 512.1715 (M + Na)+.
Figure imgf000236_0002
[00548] p-methoxyphenyl-O-di-(2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2),(1→4)- α-D- mannopyranoside (17): Compound S22f (0.125 g, 0.086 mmole) was deprotected by following general procedure 2 (method 1) to get the title compound 17 (0.42 g, 66%) as a white solid. 1H NMR (400 MHz, D2O): δ 7.10 (d, J = 8.8 Hz, 2H), 7.08 (d, J = 8.2 Hz, 2H), 5.39 (s, 1H), 4.53 (d, J = 8.2 Hz, 1H), 4.50 (d, J = 7.8 Hz, 1H), 4.25 (s, 1H), 4.20 (d, J = 7.8 Hz, 1H), 4.00 (dd, J = 3.2 and 7.2 Hz, 1H), 3.71 (s, 3H), 3.67-3.74 (m, 9H), 2.02 (s, 3H), 1.91 (s, 3H); 13C NMR (150 MHz, D2O): δ 174.48, 147.04, 154.49, 149.86, 118.53, 114.97, 100.80, 99.64, 96.55, 76.40, 75.71, 75.66, 73.74, 73.01, 72.63, 69.74, 69.27, 69.19, 67.32, 60.72, 60.60, 60.45, 59.05, 55.62, 55.34, 55.22, 22.24, 22.01; ESI-MS: m/z calcd for C29H44N2O17; 693.2713 found 693.2688 (M + H)+.
Figure imgf000237_0001
[00549] p-methoxyphenyl-O-di-(2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2),(1→6)- α-D- mannopyranoside (18): Compound S22h (0.200 g, 0.138 mmole) was deprotected by following general procedure 2 (method 1) to get the title compound 18 (0.60 g, 63%) as a white solid. 1H NMR (400 MHz, D2O): δ 7.10 (d, J = 8.8Hz, 2H), 6.96 (d, J = 8.2 Hz, 2H), 5.44 (s, 1H), 4.60 (d, J = 7.5Hz, 1H), 4.52 (d, J = 7.3Hz, 1H), 4.31 (s, 1H), 4.18 (d, J = 2.8 Hz, 1H), 3.90 (t, J = 10.7 Hz, 2H), 3.80 (s, 3H), 3.77-3.70 (m, 7H), 3.56-3.44 (m, 8H), 2.02 (s, 6H); 13C NMR (150 MHz, CHCl3): δ 172.7, 171.9, 157.9, 150.3, 118.5, 114.9, 100.2, 99.4, 99.0, 75.74, 74.2, 73.9, 72.1, 70.3, 68.7, 68.3, 68.2, 55.9, 55.6, 55.1, 20.1; ESI-MS: m/z calcd for C29H44N2O17; 692.2532 found 715.2518 (M + Na)+.
Figure imgf000237_0002
[00550] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(2- acetamido-2-deoxy-β-D-glucopyranosyl)-(1→4)-α-D-mannopyranoside (19): A mixture of S22f (0.610 g, 0.421 mmol) and 10 mL of ethylene diamine: nBuOH (1:4) was stirred at 90 oC for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac2O/pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by flash column chromatography (acetone: toluene, 2/8, v/v). The product was dissolved in 10 mL MeOH: H2O: HCOOH (6:3:1), Pd(OH)2 (50% by weight) was added and the reaction mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent, and the product was the lyophilized to get 19 (0.210 g, 67%) as a white color powder. 1H NMR (400 MHz, D2O): δ 7.01 (d, J = 9.2 Hz, 2H), 6.90 (d, J = 9.8 Hz, 2H), 5.40 (s, 1H), 4.61 (d, J = 8.0 Hz, 1H), 4.52 (d, J = 8.4 Hz, 1H), 4.25 (d, J = 2.1 Hz, 1H), 4.73 (dd, J = 1.2 & 7.2 Hz, 1H), 3.92 (d, J = 12.3 Hz, 1H), 3.74 (s, 3H), 3.72-3.67 (m, 8H), 3.60-3.41 (m, 7H), 2.12 (s, 3H), 2.03 (s, 6H); 13C NMR (150 MHz, D2O): δ 174.67, 17417, 172.91, 154.43, 149.58, 118.53, 118.37, 114.81, 101.48, 99.70, 96.04,77.51, 76.00, 75.75, 73.50, 73.39, 71.74, 71.06, 70.93, 69.57, 69.34, 68.04, 60.58, 60.47, 60.00, 55.55, 55.39, 55.13, 22.24, 21.95, 20.17, 20.03; ESI-MS: m/z calcd for C31H46N2O18 ; 735.2818 found 735.2780 (M + H)+.
Figure imgf000238_0001
[00551] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(2- acetamido-2-deoxy-β-D-glucopyranosyl)-(1→6)-α-D-mannopyranoside (20): A mixture of S22h (0.350 g, 0.241 mmol) and 10 mL of ethylene diamine: nBuOH (1:4) was stirred at 90 oC for overnight. Volatiles were then evaporated and the crude product was reacted with 10 mL Ac2O/pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by flash column chromatography (acetone: toluene, 2/8, v/v). The product was dissolved in 10 mL MeOH: H2O: HCOOH (6:3:1), Pd (OH)2 (50% by weight) was added and the reaction mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent, and the product was the lyophilized to get 20 (0.120 g, 70%) as a white color powder. 1H NMR (400 MHz, D2O): δ 7.08 (d, J = 8.4 Hz, 2H), 6.91 (d, J = 8.2 Hz, 2H), 5.38 (s, 1H), 4.66 (d, J = 8.0 Hz, 1H), 4.48 (d, J = 8.2 Hz, 1H), 4.38-4.27 (m, 2H), 4.19 (t, J = 2.8 Hz, 1H), 4.09 (d, J = 12.2 Hz, 1H), 3.98 (dd, J = 2.8 and 7.8 Hz, 1H), 3.84 (d, J = 12.3 Hz, 2H), 3.75 (s, 3H), 3.67- 3.33 (m, 11H), 1.93 (s, 3H), 1.91 (s, 3H), 1.78 (s, 3H); 13C NMR (150 MHz, D2O): δ 174.41, 173.93, 173.75, 154.47, 149.86, 118.53, 118.48, 114.93, 100.84, 99.71, 96.50, 76.76, 75.66, 73.75, 73.27, 72.74, 72.60, 69.76, 69.47, 69.24, 69.12, 67.28,62.94, 60.62, 55.60, 55.32, 55.22, 22.30, 22.06, 20.03; ESI-MS: m/z calcd for C31H46N2O18; 735.2818 found 735.2769 (M + H)+.
[00552] Preparation of linear module. As depicted in scheme S23, the preparation of linear modules was commensed with enzymatic β-1,4-galctosylation of GlcNAc residue of acceptor 16 to form LacNAc moiety 21. Modules 21 was then underwent action of α-1,3- fucosyltransferase, α-2,6- sialyltransferase, α-2,3- sialyltransferase, and α-1,3- fucosyltransferase to obtain modules 22, 23, 24, and 25 respectively. Presnece of α-1,3 fucose residue on GlcNAc restrict addition of sialic acid on adjacent galactose at both 3 and 6 positions. Interstingly, α-2,3-sialylated LacNAc 24 was found to be the substarte of α-1,3- fucosyltransferase to get 25, but not the α-2,6-sialylated LacNAc 23. More striking to us was the α-1,2- fucosylated LacNAc 26 was the substarte of α-2,6- sialyltransferase, but not of α- 2,3- sialyltransferase. Unique substrate specificities of FucTs and SiaTs allowed us to establish a rapid access to more diverse type of modules for N-glycan synthesis.
Figure imgf000240_0001
[00553] Scheme S23 | Preparation of linear modules. i, UDP-galactose, β 1, 4-GalT; ii, GDP- fucose, α 1, 3-FucT; iii, CMP-Neu5Ac, α 2, 6-SiaT; iv, CMP-Neu5Ac, α 2, 3-SiaT; v, GDP- fucose, α1, 2- FucT.
Figure imgf000240_0002
[00554] p-methoxyphenyl-O-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→2)-α-D-mannopyranoside (21): Compound 16 (100 mg, 0.204 mmol) was galactosylated by using general procedure 4 to get 21 (115 mg, 86 %) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.10 (d, J = 8.8 Hz, 2H), 6.96 (d, J = 8.1 Hz, 2H), 5.44 (s, 1H), 4.59 (d, J = 8.4 Hz, 1H), 4.49 (d, J = 8.2 Hz, 1H), 4.45 (s, 1H), 4.00-3.75 (m, 17H), 3.60 (s, 3H), 2.01 (s, 3H); ESI-MS: m/z calcd for C27H41NO17; 652.2447 found 674.2262 (M + H)+.
Figure imgf000241_0001
[00555] p-methoxyphenyl-O-β-D-galactopyranosyl-(1→4)-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-α-D-mannopyranoside (22): Compound 21 (80 mg, 0.122 mmol) was fucosylated by using general procedure 5 to afford 22 (82 mg, 84%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.15 (d, J = 9.2 Hz, 2H), 7.00 (d, J = 9.1 Hz, 2H), 5.45 (s, 1H), 5.12 (d, J = 4.1 Hz, 1H), 4.67 (d, J = 7.8 Hz, 2H), 4.44 (d, J = 8.4 Hz, 1H), 4.05 (s, 1H), 4.01 (dd, J = 3.2 and 7.8 Hz, 1H), 3.98 (t, J = 10.2 Hz, 2H), 3.80-3.70 (m, 6H), 3.79 (s, 3H), 3.70-3.40 (m, 11H), 2.06 (s, 3H), 1.18 (d, J = 6.4 Hz, 3H); ESI-MS: m/z calcd for C33H51NO21; 797.7570 found 820.2837 (M + Na)+.
Figure imgf000241_0002
[00556] p-methoxyphenyl-O-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2)-α-D-mannopyranoside (23): Compound 21 (150 mg, 0.184 mmol) was α 2,6-sialylated by using general procedure 3 to afford 23 (169 mg, 90%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.10 (d, J = 9.2 Hz, 2H), 7.08 (d, J = 9.1 Hz, 2H), 5.49 (s, 1H), 4.64 (d, J = 8.1 Hz), 1H, 4.40 (d, J = 8.2 Hz, 1H), 4.26 (t, J = 2.1 Hz, 1H), 4.01-3.80 (m, 7H), 3.74 (s, 3H), 3.66-3.58 (m, 20H), 2.63(dd, J = 4.4 and 12.8 Hz, 1H), 2.07 (s, 3H), 1.97 (s, 3H), 1.68 (t, 1H); ESI-MS: m/z calcd for C38H58N2O25; 942.3245 found 941.3269 (M - H)-.
Figure imgf000242_0001
[00557] p-methoxyphenyl-O-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→3)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl- (1→2)-α-D-mannopyranoside (24): Compound 21 (10 mg, 15.3 µ mol) was α 2,3-sialylated by using general procedure 3 to afford 24 (11.5 mg, 80%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.16 (d, J = 9.2 Hz, 2H), 7.03 (d, J = 9.5 Hz, 2H), 5.49 (s, 1H), 4.67 (d, J = 8.4 Hz, 1H), 4.56 (d, J = 8.4 Hz, 1H), 4.32 (t, J = 2.1 Hz, 1H), 4.15 (dd, J = 3.2 & 7.5 Hz, 1H), 4.10-3.98 (m, 4H), 3.95-3.85 (m, 6H), 3.84 (s, 3H), 3.80- 3.50 (m, 13H), 2.79 (dd, J = 4.8 and 12.1 Hz, 1H), 2.09 (s, 3H), 2.07 (s, 3H), 1.85 (t, 1H); ESI-MS: m/z calcd for C38H58N2O25; 942.3245 found 941.3312 (M-H)-.
Figure imgf000242_0002
[00558] p-methoxyphenyl-O-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→3)-β-D-galactopyranosyl-(1→4)-[α-L-fucopyranosyl-(1→3)-2- acetamido-2- deoxy-β-D-glucopyranosyl]-(1→2)-α-D-mannopyranoside (25): Compound 24 (8 mg, 8.5 μmol) was fucosylated by using general procedure 5 to afford 25 (6.5 mg, 70%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.14 (d, J = 6.8 Hz, 2H), 6.98 (d, J = 7.2 Hz, 2H), 5.46 (s, 1H), 5.12 (d, J = 4.2 Hz, 1H), 4.67 (d, J = 8.4 Hz, 1H), 4.30 (t, J = 2.3 Hz, 1H), 4.10 (dd, J = 3.0 & 7.8 Hz, 1H), 4.00-3.80 (m, 14H), 3.79 (s, 3H), 3.75-3.50 (m, 13H), 2.75 (dd, J = 4.0 and 12.0 Hz, 1H), 2.03 (s, 3H), 2.01(s, 3H), 1.76 (t, 1H), 1.17 (d, 3H, Fuc-Me); ESI-MS: m/z calcd for C44H68N2O29; 1088.3857 found 1087.3850 (M - H)-.
Figure imgf000243_0001
[00559] p-methoxyphenyl-O-[α-L-fucopyranosyl-(1→2)-β-D-galactopyranosyl]-(1→4)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-α-D-mannopyranoside (26): Compound 21 (3 mg, 4.6 μmol) was fucosylated by using general procedure 5 to afford 26 (2.1 mg, 53%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.17 (d, J = 7.2 Hz, 2H), 7.01 (d, J = 10.1 Hz, 2H), 5.49 (s, 1H), 5.33 (s, 1H), 4.67 (d, J = 8.2 Hz, 1H), 4.56 (d, J = 8.2 Hz, 1H), 4.33 (m, 1H), 4.25 (q, 1H), 3.98 (dd, J = 3.1 and 7.2 Hz, 1H), 3.96 (dd, J = 1.8 and 7.2 Hz, 1H), 3.85-3.50 (m, 20H), 3.40 (m, 1H), 1.97 (s, 3H), 1.14 (d, J = 6.4 Hz, 3H); ESI-MS: m/z calcd for C33H51NO21; 797.2954 found 820.2922 (M + Na)+.
Figure imgf000243_0002
[00560] p-methoxyphenyl-O-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano- sylonate-(2→6)-[α-L-fucopyranosyl-(1→2)-β-D-galactopyranosyl]-(1→4)-2- acetamido-2- deoxy-β-D-glucopyranosyl]-(1→2)-α-D-mannopyranoside (27): Compound 26 (2.0 mg, 2.7 µmol) was α 2,6-sialylated by using general procedure 3 to afford 27 (1.8 mg, 66%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.08 (d, J = 9.5 Hz, 2H), 6.91 (d, J = 9.2 Hz, 2H), 5.49 (s, 1H), 5.27 (s, 1H), 4.59 (d, J = 8.2 Hz, 1H), 4.47 (d, J = 8.1 Hz, 1H), 4.22 (bs, 1H), 4.12 (d, J = 6.8 Hz, 1H), 4.00-3.49 (m, 30H), 2.63 (dd, J = 3.2 and 12.0 Hz, 1H), 2.01(s, 3H), 1.97 (s, 3H), 1.67 (t, 1H), 1.19 (d, 3H, Fuc-Me); ESI-MS: m/z calcd for C44H68N2O29; 1088.3857 found 1087.3814 (M - H)-.
[00561] Preparation of symmetrically branched modules.
Figure imgf000244_0001
[00562] . i, β-l, 4 GalT, UDP-Gal; ii, α1,3- fucosyltransferase, GDP-fucose; iii, α2,6- sialyltransferase, CMP-β-D-Sialic acid.
Figure imgf000244_0002
[00563] Compound 28 and 29: Compound 17 (10 mg, 14.3 µmol) and 18 (10 mg, 14.3 µmol) were galactosylated by using general procedure 4 to get 28 (10 mg, 71%) and 29 (9 mg, 61%) as amorphous white solids.
[00564] p-methoxyphenyl-O-di-[β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2), (1→4)-α-D-mannopyranoside (28): 1H NMR (400 MHz, D2O): δ 7.11 (d, J = 9.2 Hz, 2H), 6.95 (d, J= 8.5 Hz, 2H), 5.44 (s, 1H), 4.65 (d, J = 8.9 Hz, 1H), 4.58 (d, J = 9.2 Hz, 1H), 4.45 (dd, J = 3.8 & 9.2 Hz, 2H), 4.30 (t, J = 2.1 & 6.5 Hz, 1H), 4.18 (dd, J = 3.2 & 7.8 Hz, 1H), 4.00 (t, J = 10.8 Hz, 2H), 3.90 (d, J = 8.2 Hz, 2H), 3.78 (s, 3H), 3.75- 3.64 (m, 20H), 3.58-3.49 (m, 4H), 2.02 (s, 3H), 2.01 (s, 3H); ESI-MS: m/z calcd for
C41H64N2O27; 1016.9564 found 1039.3607 (M + Na)+. [00565] p-methoxyphenyl-O-di-[β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2), (1→6)-α-D-mannopyranoside (29): 1H NMR (400 MHz, D2O): δ 7.02 (d, J = 9.0 Hz, 2H), 6.92 (d, J = 9.0 Hz, 2H), 5.32 (s, 1H), 4.55 (d, J = 4.3 Hz, 1H), 4.41 (d, J = 8.2 Hz, 1H), 4.34 (dd, J = 13.1, 7.9 Hz, 2H), 4.16 (s, 1H), 4.00 (d, J = 11.0 Hz, 1H), 3.843.95 (m, 2H), 3.70-3.81 (m, 9H), 3.49-3.68 (m, 16H), 3.37-3.44 (m, 4H), 1.94 (s, 3H), 1.82 (s, 3H); ESI-MS: m/z calcd for C41H64N2NaO27; 1039.3594 found 1039.3551.
Figure imgf000245_0001
[00566] Compound 30 and 31: Compound 28 (8 mg, 7.3 μmol) and 29 (8 mg, 7.3 μmol) were sialylated by using general procedure 3 to afford 30 (9 mg, 78%) and 31 (7.5 mg, 65%) as a white solid after lyophilization.
[00567] p-methoxyphenyl-O-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2), (1→4)-α-D-mannopyranoside (30): 1H NMR (400 MHz, D2O): δ 7.12 (d, J = 9.8 Hz, 2H), 6.98 (d, J = 9.3 Hz, 2H), 5.46 (s, 1H), 4.63 (d, J = 8.4 Hz, 1H), 4.58 (d, J = 8.2 Hz, 1H), 4.42 (d, J = 7.8 Hz, 2H), 4.32 (t, J = 3.2 Hz, 1H), 4.20 (dd, J = 3.2 & 7.2 Hz, 1H, 4.03-3.85 (m, 4H), 3.82-3.40 (m, 43H), 2.58 (dd, 2H, J = 3.2 & 10.3 Hz), 2.05 (s, 3H), 2.04 (s, 3H), 2.02 (s, 3H), 2.00 (s, 3H), 1.53 (m, 2H) ; ESI-MS: m/z calcd for
C63H98N4O43; 1599.4620 found 798.2775 (M - H)2-.
[00568] p-methoxyphenyl-O-di-[5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2), (1→5)-α-D-mannopyranoside (31): 1H NMR (600 MHz, D2O): δ 7.05 (d, J = 9.2 Hz, 2H), 6.95 (d, J = 9.2 Hz, 2H), 5.36 (d, J = 1.6 Hz, 1H), 4.59 (d, J = 8.2 Hz, 1H), 4.46 (d, J = 8.1 Hz, 1H), 4.36 (d, J = 7.9 Hz, 1H), 4.32 (d, J = 7.9 Hz, 1H), 4.20 (dd, J = 3.4, 1.8 Hz, 1H), 4.06 (d, J = 10.3 Hz, 1H), 3.86-3.98 (m, 4H), 3.64-3.86 (m, 19H), 3.53- 3.62 (m, 13H), 3.37-3.50 (m, 9H), 2.58 (ddd, J = 12.0, 4.4, 2.1 Hz, 2H), 1.98 (s, 3H), 1.94 (s, 3H), 1.94 (s, 3H), 1.87 (s, 3H), 1.63 (td, J = 12.2, 8.6 Hz, 2H); ESI-MS : m/z calcd for C63H98N4NaO43; 1621.5479 found 1621.5473.
Figure imgf000246_0001
[00569] p-methoxyphenyl-O-di-{β-D-galactopyranosyl-(1→4)-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]}-(1→2),(1→4)-α-D-mannopyranoside (32):
Compound 28 (15 mg, 14.7 µmol) was fucosylated by using general procedure 5 to get 32 (14 mg, 73%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.13 (d, J = 9.2 Hz, 2H), 6.99 (d, J = 9.0 Hz, 2H), 5.44 (d, J = 3.2 Hz, 1H), 5.12 (d, J = 4.1 Hz, 1H), 5.10 (d, J = 4.0 Hz, 1H), 4.81 (d, J = 8.4 Hz, 2H), 4.68 (d, J = 7.4 Hz, 1H), 4.58 (d, J = 7.2 Hz, 1H), 4.45 (dd, J = 3.2 & 8.4 Hz, 2H), 4.31 (t, J = 3.2 Hz, 1H), 4.20 (dd, J = 3.2 & 8.4 Hz, 1H), 4.09- 3.84 (m, 14H), 3.82 (s, 3H), 3.80-3.40 (m, 14H), 2.06 (s, 6H), 1.17 (d, J = 6.4 Hz, 6H); ESI- MS: m/z calcd for C53H84N2O35; 1308.4855 found 1309.4911 (M + H)+.
Figure imgf000247_0001
[00570] p-methoxyphenyl-O-di-{β-D-galactopyranosyl-(1→4)-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]}-(1→2),(1→6)-α-D-mannopyranoside (33):
Compound 29 (15 mg, 14.7 µmol) was fucosylated by using general procedure 5 to get 33 (15.5 mg, 81%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.17 (d, J = 8.2 Hz, 2H), 7.06 (d, J = 8.0 Hz, 2H), 5.42 (s, 1H), 5.14 (d, J = 4.0 Hz, 1H), 5.09 (d, J = 4.0 Hz, 1H), 4.87-4.85 (m, 2H), 4.60 (d, J = 7.2 Hz, 1H), 4.56 (q, 2H), 4.30 (m, 1H), 4.15 (d, J = 12.2 Hz, 1H), 4.06 (dd, J = 3.2 & 7.8 Hz, 1H), 4.00-3.45 (m, 37), 2.06 (s, 3H), 1.95 (s, 3H), 1.19 (d, J = 6.5 Hz, 6H) ; ESI- MS : m/z calcd for C53H84N2O35; 1308.4855 found 1331.3561 (M + Na)+.
[00571] Preparation of asymmetrically branched module.
Figure imgf000247_0002
[00572] Scheme S25 | Preparation of assymetric module. UDP-galactose, β 1, 4-GalT; ii, GDP-fucose α1, 3-FucT; iii, CMP-Neu5Ac, α2, 6-SiaT; vi, NaOH.
Figure imgf000248_0001
[00573] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(β-D-galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→4)-α-D- mannopyranoside (34): Compound 19 (15 mg, 20.4 µmol) was galactosyalated using general procedure 4 to afford the 34 (12.5 mg, 68%) as amorphous white solids. 1H NMR (600 MHz, D2O) δ 7.01 (d, J = 9.2 Hz, 2H), 6.88 (d, J = 9.2 Hz, 1H), 5.34 (d, J = 1.8 Hz, 1H), 4.56 (d, J = 8.5 Hz, 1H), 4.45 (d, J = 8.1 Hz, 1H), 4.37 (d, J = 7.7 Hz, 1H), 4.20-4.33 (m, 2H), 4.16-4.20 (m, 1H), 4.07 (dd, J = 8.7, 3.0 Hz, 1H), 3.86-3.94 (m, 1H), 3.81 (d, J = 3.4 Hz, 1H), 3.31-3.78 (m, 21H), 2.03 (s, 3H), 1.93 (s, 3H), 1.92 (s, 3H); ESI-MS: m/z calcd for
C37H56N2NaO23; 919.9166 found 919.3156.
Figure imgf000248_0002
[00574] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(β-D-galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→6)-α-D- mannopyranoside (S27a): Compound 20 (8 mg, 10.9 µmol) was galactosylated by using general procedure 4 to give the 35 (5 mg, 75 %) as amorphous white solids. 1H NMR (600 MHz, D2O): δ 7.12 (d, J = 9.1 Hz, 2H), 7.01 (d, J = 9.8 Hz, 2H), 5.40 (s, 1H), 4.67 (d, J = 8.4 Hz, 1H), 4.49 (d, J = 8.4 Hz, 1H), 4.40 (d, J = 8.3 Hz, 2H), 4.31 (dd, J = 3.1 & 7.8 Hz, 1H), 4.21 (t, J = 3.1 Hz, 1H), 4.08 (d, J = 12.3 Hz, 2H), 4.00 (dd, J = 3.2 & 8.1 Hz, 1H), 3.90-3.48 (m, 3H), 3.80 (s, 3H), 3.75-3.47 (m, 16H), 2.15 (s, 3H), 2.0 (s, 3H), 1.98 (s, 3H); ESI-MS: m/z calcd for C37H56N2O23; 896.3162 found 919.3164 (M +Na)+.
Figure imgf000249_0001
[00575] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D- galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→4)-α-D- mannopyranoside (36): Compound 34 (10 mg, 11.1 µmol) was α 2,6-sialylated by using general procedure 3 to afford 36 (11.2 mg, 84%) as white solid after lyophilization. 1H NMR (600 MHz, D2O): δ 7.02 (d, J = 9.2 Hz, 2H), 6.89 (d, J = 9.2 Hz, 2H), 5.35 (d, J = 2.0 Hz, 1H), 4.55 (dd, J = 18.4, 8.4 Hz, 1H), 4.48 (d, J = 7.9 Hz, 1H), 4.17-4.37 (m, 4H), 4.05-4.12 (m, 1H), 3.29-3.97 (m, 36H), 2.56 (dd, J = 12.4, 4.7 Hz, 1H), 2.04 (s, 3H), 1.96 (s, 3H), 1.92 (s, 3H), 1.92 (s, 3H), 1.60 (t, J = 12.2 Hz, 1H); ESI-MS: m/z calcd for C48H72N3O31;
1186.4155 found 1186.4175.
Figure imgf000249_0002
[00576] p-methoxyphenyl-O-(4-O-acetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)- O-(5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D- galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→6)-α-D- mannopyranoside (37): Compound 35 was α2,6-sialylated by using general procedure 3 to afford 37 (5.1 mg, 77%) as white solid after lyophilization. 1H NMR (600 MHz, D2O): δ 7.11 (d, J = 9.1 Hz, 2H), 7.00 (d, J = 9.2 Hz, 2H), 5.38 (s, 1H), 4.50 (d, J = 8.4 Hz, 1H), 4.36 (d, J = 8.2 Hz, 1H), 4.22 (t, J = 2.1 Hz, 1H), 4.10 (dd, J = 3.1 & 7.8 Hz, 1H), 3.97-3.85 (m, 4H), 3.77 (s, 3H), 3.73-3.46 (m, 25H), 2.63 (dd, J = 3.2 and 7.8 Hz, 1H), 2.09 (s, 3H), 2.01 (s, 3H), 1.99 (s, 3H), 1.94 (s, 3H), 1.65 (t, 1H); ESI-MS: m/z calcd for C48H73N3O31;
1187.4144 found 1186.4133 (M -H)-.
Figure imgf000250_0001
[00577] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D- glucopyranosyl)-(1→2)-O-(5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D- glucopyranosyl)-(1→4)-α-D-mannopyranoside (40): To a solution of compound 36 (7 mg, 5.8 µmol) in 0.5 mL H2O was added NaOH (9.4 mg, 23.6 µmol) and stirred for 4 h.
Reaction was neutralized and product was putified by Bio-Gel P-2 chromatography (eluent H2O) to afford 38 (6.1 mg, 89%) as white solid after lyophilization. Compound 38 (6 mg, 5.3 µmol) and UDP galactose (6.4 mg, 10.6 µmol) were dissolved in Tris buffer (25 mM, pH 7.5) and MnCl2 (20 mM). GalT-1 (150 units) were added to achieve a final concentration of glycan to 5 mM. The resulting reaction mixture was incubated at 37 °C for 48 h. The reaction mixture was centrifuged and the supernatant subjected to gel filtration over P2- Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the 40 (5 mg, 73%) as amorphous white solids. 1H NMR (400 MHz, D2O) δ 7.02 (d, J = 9.2 Hz, 2H), 6.88 (d, J = 9.2 Hz, 2H), 5.35 (d, J = 1.8 Hz, 1H), 4.56 (d, J = 7.9 Hz, 1H), 4.48 (d, J = 7.9 Hz, 1H), 4.35 (dd, J = 9.6, 7.7 Hz, 2H), 4.27-4.30 (m, 2H), 4.21-4.24 (m, 1H), 4.02-4.20 (m, 6H), 3.87-3.92 (m, 3H), 3.39-3.85 (m, 28H), 2.56 (dd, J = 12.4, 4.6 Hz, 1H), 1.96 (s, 3H), 1.93 (s, 3H), 1.92 (s, 3H), 1.60 (t, J = 12.2 Hz, 1H); ESI-MS: m/z calcd for C52H80N3O35; 1306.4578 found 1306.4617.
Figure imgf000251_0001
[00578] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D- glucopyranosyl)-(1→2)-O-(5-Acetamido-3,5-dideoxy-D-glycero-α-D-galacto-2- nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→6)-O-2-acetamido-2-deoxy-β-D- glucopyranosyl)-(1→4)-α-D-mannopyranoside (41): To a solution of compound 37 (5 mg, 4.2 µmol) in 0.5 mL H2O was added NaOH (6.7 mg, 16.8 µmol) and stirred for 4 h.
Reaction was neutralized and product was purified by Bio-Gel P-2 chromatography (eluent H2O) to afford 39 (3.8 mg, 79%) as white solid after lyophilization. Compound 39 (3.5 mg, 3.0 µmol) and UDP galactose (3.9 mg, 6.1 µmol) were dissolved in Tris buffer (25 mM, pH 7.5) and MnCl2 (20 mM). GalT-1 (150 units) were added to achieve a final concentration of glycan to 5 mM. The resulting reaction mixture was incubated at 37 °C for 48 h. The reaction mixture was centrifuged and the supernatant subjected to gel filtration over P2- Biogel (eluent water). Fractions containing the product were combined and lyophilized to give the 41 (3.3 mg, 75%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.11 (d, J = 9.1 Hz, 2H), 7.00 (d, J = 9.2 Hz, 2H), 5.38 (s, 1H), 4.64 (d, J = 8.1 Hz, 1H), 4.50 (d, J = 8.2 Hz, 1H), 4.23 (d, J = 8.3 Hz, 1H), 4.38 (d, J = 8.0 Hz, 1H), 4.22 (t, J = 2.1 Hz, 1H), 4.10 (d, J = 12.2 Hz, 1H), 4.01-3.95 (m, 4H), 3.87-3.63 (m, 26H), 3.52-3.45 (m, 8H), 2.63 (dd, J = 2.1 and 7.8 Hz, 1H), 2.63 (dd, J = 3.2 and 7.8 Hz, 1H), 2.01 (s, 3H), 1.99 (s, 3H), 1.93 (s, 3H), 1.67 (t, 1H); ESI-MS: m/z calcd for C52H81N3O35; 1307.4567 found 1306.4609 (M - H)-.
Figure imgf000252_0001
[00579] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-O-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-O-(5-Acetamido-3,5-dideoxy-D-glycero-α- D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-O-2-acetamido-2- deoxy-β-D-glucopyranosyl)-(1→4)-α-D-mannopyranoside (42): Compound 40 (2 mg, 1.52 µmol) was α1,3-fucosylated by using general procedure 5 to get 42 (2 mg, 85%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.16 (d, J = 8.8 Hz, 2H), 7.06 (d, J = 8.1 Hz, 2H), 5.45 (s, 1H), 5.08 (d, J = 4.1 Hz, 1H), 4.60 (d, J = 4.2 Hz, 1H), 4.44 (dd, J = 3.5 & 7.9 Hz, 2H), 4.30 (bs, 1H), 4.15 (d, J = 8.4 Hz, 1H), 4.09-3.40 (m, 40H), 2.70 (d, J = 11.2 Hz, 1H), 2.08 (s, 3H), 2.05 (s, 3H), 1.93 (s, 3H), 1.74 (t, 1H), 1.20 (d, J = 6.4 Hz, 3H); ESI- MS: m/z calcd for C58H91N3O39; 1453.5245 found 1452.5157 (M -H)-.
Figure imgf000252_0002
[00580] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-O-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-O-(5-Acetamido-3,5-dideoxy-D-glycero-α- D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-O-2-acetamido-2- deoxy-β-D-glucopyranosyl)-(1→6)-α-D-mannopyranoside (43): Compound 41 (4 mg, 3.05 µmol) was α 1,3-fucosylated by using general procedure 5 to get 43 (3.2 mg, 72%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.21 (d, J = 8.2 Hz, 2H), 7.06 (d, J = 8.0 Hz, 2H), 5.74 (s, 1H), 5.72 (d, J = 8.1 Hz, 2H), 5.52 (dd, J = 3.1 & 7.2 Hz, 1H), 5.40 (s, 1H), 5.01 (d, J = 4.2 Hz, 1H), 4.50-3.25 (m, 42H), 2.50 (dd, J = 3.1 & 7.2 Hz, 1H), 2.01 (s, 3H), 1.99 (s, 6H), 1.56 (t, 1H), 1.05 (d, 3H, Fuc-Me); ESI-MS: m/z calcd for C58H91N3O39; 1453.5245 found 1452.5445 (M - H)-.
Figure imgf000253_0001
[00581] p-methoxyphenyl-O-(2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)-O-(β-D- galactopyranosyl-(1→4)-O-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→6)-α-D- mannopyranoside (44): To a solution of compound 35 (20 mg, 22.3 µmol) in 0.5 mL H2O was added NaOH (3.57 mg, 89.2 µmol) and stirred for 4 h. Reaction was neutralized and product was purified by Bio-Gel P-2 chromatography (eluent H2O) to afford 44 (15.3 mg, 80%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.15 (d, J = 9.2 Hz, 2H), 7.06 (d, J = 9.8 Hz, 2H), 5.42 (s, 1H), 4.67 (d, J = 8.2 Hz, 1H), 4.54 (d, J = 8.0 Hz, 1H), 4.47(d, J = 8.2 Hz, 1H), 4.32 (t, J = 2.1 Hz, 1H), 4.10 (d, J = 12.2 Hz, 1H), 4.09 (dd, J = 3.2 & 8.2 Hz, 1H), 4.01-3.91(m, 4H), 3.85 (s, 3H), 3.80-3.40 (m, 21H), 2.03 (s, 3H), 1.98 (s, 3H); ESI-MS: m/z calcd for C35H54N2O22; 854.3125 found 877.3062 (M +Na)+.
Figure imgf000253_0002
[00582] p-methoxyphenyl-O-(2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)-O-(β-D- galactopyranosyl-(1→4)-O-[α-L-fucopyranosyl-(1→3)-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→6)-α-D-mannopyranoside (45): Compound 44 (8 mg, 9.3 µmol) was α 1,3-fucosylated by using general procedure 5 to afford 45 (6 mg, 66%) as white solid after lyophilization. 1H NMR (400 MHz, D2O): δ 7.14 (d, J = 8.2 Hz, 2H), 7.02 (d, J = 8.1 Hz, 2H), 5.41 (s, 1H), 5.07 (d, J = 4.0 Hz, 1H), 4.64 (d, J = 8.2 Hz, 2H), 4.58 (d, J = 7.4 Hz, 1H), 4.44 (d, J = 8.5 Hz, 1H), 4.28 (t, J = 2.1 Hz, 1H), 4.10 (d, J = 12.2 Hz, 1H), 4.05 (dd, J = 3.1 & 7.2 Hz, 1H), 3.95-3.85 (m, 8H), 3.82 (s, 3H), 3.80-3.33 (m, 17H), 2.04 (s, 3H), 1.93 (s, 3H), 1.17 (d, J = 6.8 Hz, 3H); ESI-MS: m/z calcd for C41H64N2O26; 1000.2356 found 1023.3599 (M + Na)+.
Figure imgf000254_0001
[00583] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl)-(1→2)-O-(β-D-galactopyranosyl-(1→4)-O-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→6)-α-D-mannopyranoside (46): Compound 45 (7 mg, 7.2 µmol) was β 1,4-galactosylated by using general procedure 4 to give the 46 (6.5 mg, 80 %) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.16 (d, J = 9.4 Hz, 2H), 7.05 (d, J = 9.3 Hz, 2H), 5.43 (s, 1H), 5.09 (d, J = 4.2 Hz, 1H), 4.83 (d, J = 7.5 Hz, 1H), 4.78 (d, J = 7.2 Hz, 1H), 4.58 (d, J = 8.2 Hz, 1H), 4.48 (d, J = 9.5 Hz, 1H), 4.42 (d, J = 8.5 Hz, 1H), 4.30 (dd, J = 2.1 & 3.4 Hz, 1H), 4.14 (s, 1H), 4.09-3.92 (m, 14H), 3.85 (s, 3H), 3.84-3.50 (m, 17H), 2.06 (s, 3H), 1.95 (s, 3H), 1.20 (d, J = 6.5 Hz.3H); ESI-MS: m/z calcd for C47H74N2O31; 1162.4309 found 1185.4076 (M +Na)+.
Figure imgf000255_0001
[00584] p-methoxyphenyl-O-(β-D-galactopyranosyl-(1→4)-O-[α-L-fucopyranosyl-(1→3)-2- acetamido-2-deoxy-β-D-glucopyranosyl]-(1→6)-O-(5-Acetamido-3,5-dideoxy-D-glycero-α- D-galacto-2-nonulopyrano-sylonate-(2→6)-β-D-galactopyranosyl-(1→4)-O-2-acetamido-2- deoxy-β-D-glucopyranosyl)-(1→2)-α-D-mannopyranoside (47): Compound 46 (5 mg, 4.31 µmol) was α2,6-sialylated by using general procedure 3 to get 47 (5.2 mg, 83%) as amorphous white solids. 1H NMR (400 MHz, D2O): δ 7.08 (d, J = 8.1 Hz, 2H), 6.97 (d, J = 8.0 Hz, 2H), 5.48 (s, 1H), 5.10 (d, J = 5.1 Hz, 1H), 4.50 (d, J = 7.2 Hz, 1H), 4.43 (dd, J = 3.1 & 8.2 Hz, 2H), 4.32 (bs, 1H), 4.08 (d, J = 8.1 Hz, 1H), 4.09-3.40 (m, 41H), 2.60 (dd, J = 3.2 & 9.2 Hz, 1H), 1.97 (s, 3H), 1.95 (s, 3H), 1.90 (s, 3H), 1.54 (t, 1H), 1.18 (d, J = 6.4 Hz, 3H); ESI-MS: m/z calcd for C58H91N3O39; 1453.5245 found 1452.5101 (M -H)-.
[00585] Chemical derivatization of chemo-enzymatically prepared modules. The modules 21 and 22 generated by chemo-enzymatic way were then peracetylated in presence of
Ac2O/pyridine. The reducing end p-methoxy phenyl ether protection was then cleaved using cerium ammonium nitrate and free hydroxyl was changed to fluoride to obtained donors 50 and 51 (Scheme S28).
Figure imgf000256_0001
[00586] Scheme S26 | Reagents and conditions. i, Ac2O, pyridine, RT, overnight; ii, (1) CAN, ACN: toluene: H2O, (2) DAST, CH2Cl2, -30 °C. CAN: Cerium ammonium nitrate; DAST: Diethylaminosulfur trifluoride.
Figure imgf000256_0002
[00587] p-methoxyphenyl-O-[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[3,6-O- diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-3,4,6-O-triacetyl-α-D- mannopyranoside (48): To a solution of 21 (0.230 g, 0.360 mmol) in 10 mL pyridine at 0 °C was added acetic anhydride (6 mL) and stirred at RT for overnight. Reaction mixture was then concentrated, diluted with 50 mL of CH2Cl2 and extracted with sat. NaHCO3.
Combined organic layers were evaporated and product was purified by silica gel column chromatography (0%→ 20% acetone in toluene) to afford desired 48 (0.260 g, 72 %). TLC (acetone : toluene =3/7, v/v), Rf = 0.34; 1H NMR (400 MHz, CHCl3): δ 7.00 (d, J = 9.1 Hz, 2H), 6.82 (d, J = 9.1 Hz, 2H), 5.74 (d, J = 8.7 Hz, 1H), 5.33-5.35 (m, 2H), 5.27-5.30 (m, 2H), 5.22 (dd, J = 9.6, 8.2 Hz, 1H), 5.10 (dd, J = 10.5, 7.9 Hz, 1H), 4.96 (dd, J = 10.5, 3.4 Hz, 1H), 4.72 (d, J = 7.5 Hz, 1H), 4.47 (d, J = 7.9 Hz, 1H), 4.41 (dd, J = 11.8, 2.7 Hz, 1H), 4.31 (t, J = 2.2 Hz, 1H), 3.98-4.21 (m, 6H), 3.81-3.91 (m, 2H), 3.72-3.79 (m, 4H), 3.63 (ddd, J = 8.6, 5.6, 2.7 Hz, 1H), 2.14 (s, 3H), 2.11 (s, 3H), 2.08 (s, 3H), 2.06 (s, 2H), 2.03 (s, 3H), 2.03 (s, 6H), 2.02 (s, 3H), 1.96 (s, 6H); ESI-MS: m/z calcd for C45H59NO26; 1029.9480 found 1030.4587 (M + H)+.
Figure imgf000257_0001
[00588] [2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[3,6-O-diacetyl-2-acetamido-2- deoxy-β-D-glucopyranosyl]-(1→2)-3,4,6-O-triacetyl-α-D-mannopyranosyl fluoride (50): Cerium ammonium nitrate (0.2 g, 0.554 mmol) was added to a solution of compound 48 (0.200 g, 0.203 mmol) in 10 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at RT for 3 h. The reaction was diluted with EtOAc (50 mL) and washed with H2O (30 x 2 mL) and brine (30 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by flash column chromatography (0%→ 25% acetone in toluene) to afford -OH compound (0.120 g) as a foam. The residue (0.120 g, 0.130 mmol) was dissolved in CH2Cl2 (10 mL) at -30 °C. Then, DAST (34 µL, 0.260 mmol) was added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (acetone: toluene, 3/7) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 30 mL) and brine (20 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 20% acetone in toluene) to afford 50 (0.080 g, 51% over 2 steps) as white solid. TLC (acetone: toluene =3/7, v/v), Rf = 0.34; 1H NMR (600 MHz, CHCl3): δ 5.50 (d, J = 49.6 Hz, 1H), 5.30 (d, J = 3.8 Hz, 1H), 2.26 (t, J = 7.8 Hz, 1H), 5.05-4.89 (m, 4H), 4.55 (d, J = 8.4 Hz, 1H), 4.40 (d, J = 8.2 Hz, 1H), 4.32 (s, 2H), 4.18 (dd, J = 3.2 and 7.8 Hz, 1H), 4.05-4.01 (m, 6H), 3.81 (t, J =7.8 Hz, 1H), 3.71 (t, J =7.1 Hz, 1H), 3.50 (t, J = 3.1 Hz, 1H), 2.29 (s, 3H), 2.08 (s, 3H), 2.07 (s, 3H), 2.06 (s, 3H), 2.02 (s, 3H), 1.99 (s, 3H), 1.98 (s, 3H), 1.96 (s, 3H), 1.91 (s, 3H), 1.82 (s, 3H), 13C NMR (150 MHz, CHCl3): 171.29, 171.10, 170.66, 170.56, 170.35, 170.30, 169.50, 129.21, 128.40, 125.47, 106.54, 104.31, 101.05, 100.31, 76.07, 72.82, 72.64, 72.36, 71.16, 70.95,70.71, 69.41, 69.28, 66.86, 64.92, 62.38, 62.13, 61.04, 53.12, 23.13, 21.64, 21.22, 20.95, 20.87, 20.77, 20.68, 20.62; ESI-MS: m/z calcd for C38H52FNO24; 925.8145 found 925.8354 (M +H)+.
Figure imgf000258_0001
[00589] p-methoxyphenyl-O-[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[2,3,4-O- triacetyl-α-L-fucopyranosyl-(1→3)-3,6-O-diacetyl-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2)-3,4,6-O-triacetyl-α-D-mannopyranoside (49): To a solution of 22 (0.100 g, 0.125 mmol) in 6 mL pyridine at 0 °C was added acetic anhydride (4 mL) and stirred at rt for overnight. Reaction mixture was then concentrated, diluted with 50 mL of CH2Cl2 and extracted with sat. NaHCO3. Combined organic layers were evaporated and product was purified by silica gel column chromatography (0%→ 10% acetone in CH2Cl2) to afford desired 49 (0.135 g, 85 %). TLC (acetone: CH2Cl2 =1/9, v/v), Rf = 0.31; 1H NMR (400 MHz, CHCl3): δ 7.00 (d, J = 6.8 Hz, 2H), 6.83 (d, J = 6.8 Hz, 2H), 5.43 (d, J = 3.2 Hz, 1H), 4.42 (d, J = 3.2 Hz, 1H), 3.98 (d, J = 2.1 Hz, 2H), 5.25 (dd, J = 3.2 & 8.2 Hz, 2H), 5.19 (dd, J = 3.8 & 8.5 Hz, 2H), 5.10 (t, J = 9.8 Hz, 2H), 4.89 (d, J = 6.3 Hz, 1H), 4.85 (d, J = 2.2 Hz, 1H), 4.70 (d, J = 9.8 Hz, 2H), 4.61 (d, J = 1.2 Hz, 1H), 4.40 (dd, J = 3.2 & 7.2 Hz, 1H), 4.31 (m, 3H), 4.22-3.89 (m, 6H), 3.80 (m, 2H), 3.78 (s, 3H), 3.60 (m, 1H), 2.10 (s, 3H), 2.08 (s, 3H), 2.08 (s, 3H), 2.02 (s, 3H), 2.00 (s, 3H), 1.99 (s, 3H), 1.98 (s, 3H), 1.96 (s, 3H), 1.93 (s, 3H), 1.90 (s, 3H), 1.89 (s, 3H), 1.88 (s, 3H), 1.11 (d, 3H); ESI-MS: m/z calcd for C55H73NO32; 1259.4116 found 1282.3974 (M +Na)+.
Figure imgf000259_0001
[00590] [2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[2,3,4-O-triacetyl-α-L- fucopyranosyl-(1→3)-3,6-O-diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)- 3,4,6-O-triacetyl-α-D-mannopyranosyl fluoride (50): Cerium ammonium nitrate (0.121 g, 0.142 mmol) was added to a solution of compound 49 (0.090 g, 0.071 mmol) in 7 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at rt for 3 h. The reaction was diluted with EtOAc (40 mL) and washed with H2O (10 x 2 mL) and brine (10 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by flash column chromatography (0%→ 15% acetone in CH2Cl2) to afford - OH compound (0.065 g) as a foam. The residue (0.060 g, 0.052 mmol) was dissolved in CH2Cl2 (5 mL) at -30 °C. Then, DAST (11.6 µL, 0.104 mmol) was added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (acetone: CH2Cl2, 1/9) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 10 mL) and brine (10 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by silica gel column chromatography (0%→ 10% acetone in CH2Cl2) to afford 51 (0.055 g, 67% over 2 steps) as white solid. TLC (acetone: CH2Cl2 =1/9, v/v), Rf = 0.44; 1H NMR (400 MHz, CHCl3): δ 5.55 (d, J = 52.1 Hz, 1H), 5.40 (dt, J = 3.2 & 7.8 Hz, 3H), 5.21 (dd, J = 2.1 & 8.2 Hz, 2H), 5.18-5.04 (m, 3H), 5.0 (bs, 1H), 4.60 (s, 2H), 4.40 (dd, J = 5.6 & 8.5 Hz, 1H), 4.38-4.00 (m, 7H), 3.80 (m, 2H), 3.60 (m, 1H), 2.16 (s, 3H), 2.14 (s, 3H), 2.13 (s, 3H), 2.10 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 2.06 (s, 3H), 2.06 (s, 3H), 2.05 (s, 3H), 2.04 (s, 3H), 2.00 (s, 3H), 1.95 (s, 3H), 1.94 (s, 3H), 1.17 (d, J = 6.4 Hz, 3H) ; ESI-MS: m/z calcd for C48H66FNO30; 1155.0314 found 1178.3491 (M +Na)+.
[00591] Chemical glycosylation to core trisaccharide: At this stage we are in position to investigate the coupling efficiency of fluoride donors 50 and 51 to core trisaccharide 15. Depicted in Scheme S29, stereo-selctive conjugation of 50 to 3-O position of core in presence of AgOTf/Cp2HfCl2 provided expected hexasaccharide 52 in 56% yield. The reductive cleavage of benzylidine ring using catalytic p-toluene sulfonic acid provided 4, 6-diol 53. Taking advantage of its reactivity, primary hydroxyl group of 53 was then selectively glycosylated with 51 to afford fully protected decasaccharide 54 in moderate yield. At last, the global deprotection afforded the desired selectively fucosylated bi-antennary complex type glycan 55.
Figure imgf000261_0001
[00592] Scheme S27 | Reagents and conditions. i, AgOTf, Cp2HfCl2, toluene, 4 Å MS, 0 °C to RT; ii, p-TSA, acetonitrile, RT; iii, (1) LiOH, 1,4-dioxane: H2O; 90 °C, overnight; (2) Ac2O, pyridine, overnight; (3) NaOMe, MeOH, overnight; (4) Pd(OH)2, MeOH: H2O: HCOOH (5:3:2), H2. [00593] AgOTf: Silver trifluromethanesulfonate; Cp2HfCl2: Bis(cyclopentadienyl)hafnium dichloride, MS: molecular sieves.
Figure imgf000262_0001
[00594] 5-Azidopentyl-O-{[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[3,6-O- diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-[3,4,6-O-triacetyl-α-D- mannopyranosyl]}-(1→3)-[2-O-acetyl-4,6-O-benzylidine-β-D-mannopyranosyl-(1→4)-O- (3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl)- (1→4)-O-3,6-di-O-benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D- glucopyranoside (52). A mixture of Silver triflate (0.039 g, 0.155 mmol), Bis
(cyclopentadienyl) hafnium dichloride (0.041 g, 0.108 mmol) and 4 Å activated molecular sieves in dry toluene (3 mL) was stirred at RT for 1 h. The reaction mixture was then cooled to 0 °C, a solution of donor 50 (0.043 g, 0.046 mmol) and acceptor 15 (0.045 g, 0.031 mmol) in 3 mL toluene was added. The mixture was stirred at RT for 3 h, quenched with Et3N, diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 20 mL), and a brine (20 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column
chromatography (0%→ 10% acetone in CH2Cl2) to afford 52 (0.051 g, 70%) as colorless foam. TLC: (acetone: CH2Cl2 = 1.5/8.5, v/v): Rf = 0.46; 1H NMR (400 MHz, CHCl3): δ 7.46-7.16 (m, 25H), 5.41 (s, 1H), 5.32 (d, J = 9.8 Hz, 1H), 5.29 (d, J = 7.2 Hz, 1H), 5.20 (t, J = 10.2 Hz, 1H), 5.09 (t, J = 10.3 Hz, 1H), 4.93-4.87 (m, 5H), 4.82-4.57 (m, 5H), 4.50 (d, J = 12.2 Hz, 2H), 4.41-4.22 (m, 4H), 4.13-3.56 (m, 8H), 3.43-3.36 (m, 4H), 3.20 (t, J = 10.3 Hz, 4H), 3.19 (t, J = 10.2 Hz, 1H), 2.20 (s, 3H), 2.18 (s, 3H), 2.13 (s, 3H), 2.06 (s, 3H), 2.05 (s, 3H), 2.04 (s, 3H), 2.03 (s, 3H), 1.98 (s, 3H), 1.96 (s, 3H), 1.90 (s, 3H), 1.81 (s, 3H), 1.58-1.51 (m, 4H), 1.40-1.34 (m, 2H); 13C NMR (150 MHz, CHCl3): δ 171.28, 170.80, 170.69, 170.49, 170.43, 170.36, 169.97, 169.68, 169.41, 154.30, 154.13, 138.83, 138.18, 137.44, 131.28, 129.25, 129.11, 128.91, 128.63, 128.54, 128.37, 128.18, 128.10, 128.00, 127.79, 127.71, 126.47, 102.55, 101.37, 100.84, 100.44, 98.60, 95.82, 76.07, 74.74, 74.61, 74.51, 74.19, 73.83, 73.59, 72.35, 71.24, 70.95, 70.79, 70.03, 69.62, 69.52, 69.37, 68.66, 68.42, 66.92, 66.41, 65.51, 62.42, 62.02, 61.15, 57.88, 57.23, 53.60, 51.58, 29.27, 28.82, 23.46, 23.29, 21.10, 20.96, 20.82; ESI-MS: m/z calcd for C104H126Cl6N6O41; 2360.8510 found 2361.6131 (M +H)+.
Figure imgf000263_0001
[00595] 5-Azidopentyl-O-{[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[3,6-O- diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-[3,4,6-O-triacetyl-α-D- mannopyranosyl]}-(1→3)-[2-O-acetyl-β-D-mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2- deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O- benzyl-2-deoxy-2-(2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranoside (53): p- Toluene sulfonic acid monohydrate (0.001 g, 0.008 mmol) was added to a solution of 52 (0.040 g, 0.016 mmol) in acetonitrile: MeOH 2/1 (3 mL) and the resulting reaction mixture was stirred at RT for 5 h. The reaction was quenched by adding Et3N and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% acetone in CH2Cl2) to give diol 53 (0.022 g, 57%). TLC: (acetone: CH2Cl2 = 1.5/8.5, v/v): Rf = 0.32; 1H NMR (400 MHz, CDCl3): δ 7.43-7.17 (m, 20H), 5.33 (d, J = 3.2 Hz, 1H), 5.25 (d, J = 3.2 Hz, 1H), 5.19-5.04 (m, 4H), 4.98 (d, J = 3.2 Hz, 1H), 4.95 (d, J = 3.1 Hz, 1H), 4.94-4.89 (m, 2H), 4.72-4.55 (m, 8H), 4.50-4.28 (m, 9H), 4.20-3.30 (m, 30H), 3.20 (t, 5H), 2.15 (s, 3H), 2.14 (s, 3H), 2.12 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 2.06 (s, 3H), 2.04 (s, 3H), 2.03 (s, 3H), 2.02 (s, 3H), 2.01 (s, 3H), 2.00 (s, 3H), 1.95 (s, 3H), 1.94 (s, 3H), 1.56-1.51 (m, 4H), 1.40- 1.34 (m, 2H); ESI-MS: m/z calcd for C97H122Cl6N6O43; 2272.7420 found 2295.5522 (M
Figure imgf000264_0001
[00596] 5-Azidopentyl-O-{[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[3,6-O- diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-[3,4,6-O-triacetyl-α-D- mannopyranosyl]}-(1→3)-{2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]-(1→4)-[2,3,4-O- triacetyl-α-L-fucopyranosyl-(1→3)-3,6-O-diacetyl-2-acetamido-2-deoxy-β-D- glucopyranosyl]-(1→2)-3,4,6-O-triacetyl-α-D-mannopyranosyl}-(1→6)-[2-O-acetyl-β-D- mannopyranosyl-(1→4)-O-(3,6-di-O-benzyl-2-deoxy-2-(2,2,2- trichloroethoxy)carbonylamino-β-D-glucopyranosyl)-(1→4)-O-3,6-di-O-benzyl-2-deoxy-2- (2,2,2-trichloroethoxy)carbonylamino-β-D-glucopyranoside (53): A mixture of Silver triflate (0.011 g, 44.1 µmol), Bis(cyclopentadienyl) hafnium dichloride (0.012 g, 30.8 µmol) and 4 Å activated molecular sieves in dry toluene (3 mL) was stirred at RT for 1 h. The reaction mixture was then cooled to 0 °C, a solution of donor 50 (0.015 g, 13.2 µmol) and acceptor 15 (0.020 g, 8.80 µmol) in 2 mL toluene was added. The mixture was stirred at RT for 5 h, quenched with Et3N, diluted with CH2Cl2 and filtered through Celite. The filtrate was washed with aqueous NaHCO3 (2 x 10 mL), and a brine (20 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography (0%→ 15% acetone in CH2Cl2) to afford 52 (0.010 g, 34%) as colorless foam. TLC: (acetone: CH2Cl2 = 1.5/8.5, v/v): Rf = 0.41; 1H NMR (400 MHz, CHCl3): δ 7.48-7.20 (m, 20H), 5.40-4.51 (m, 24H), 4.50-4.00 (m, 10H), 3.98-3.50 (m, 30H), 3.49-3.10 (m, 20H), 2.18 (s, 3H), 2.16 (s, 3H), 2.15 (s, 3H), 2.14 (s, 3H), 2.13 (s, 3H), 2.12 (s, 3H), 2.11 (s, 3H), 2.10 (s, 3H), 2.09 (s, 3H), 2.07 (s, 3H), 2.06 (s, 3H), 2.05 (s, 3H), 2.04 (s, 3H), 2.03 (s, 3H), 2.02 (s, 3H), 2.01 (s, 3H), 2.00 (s, 3H), 1.99 (s, 3H), 1.97 (s, 3H), 1.95 (s, 3H), 1.94 (s, 3H), 1.93 (s, 3H), 1.33-1.23 (m, 4H), 1.20-1.15 (m, 2H); ESI-MS: m/z calcd for C145H187Cl6N7O73; 3408.7670 found 1176.3855 (M +K)3+.
Figure imgf000265_0001
[00597] 5-Aminopentyl-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→2)-α-D-mannopyranosyl]-(1→3),-[β-D-galactopyranosyl-(1→4)-(α-L- fucopyranosyl-(1→3)-2-2-acetamido-2-deoxy-β-D-glucopyranosyl)-(1→2)-α-D- mannopyranosyl]-(1→6)-β-D-mannopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D- glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (55): A mixture of 54 (0.010 g, 2.9 µmol) and lithium hydroxide (0.005 g, 50% by wt) in 2 mL of 1, 4 dioxane: H2O (4:1) was stirred at 90 °C for overnight. Volatiles were then evaporated and the crude product was reacted with 3 mL Ac2O: pyridine (1:2) for overnight. The solvents were removed using high vacuum and product was purified by C18 gel column chromatography (MeOH: H2O as an eluent). The product was de-acetylated using sodium methoxide in MeOH (3 mL) for overnight. The reaction mixture was neutralized by using IR-120, filtered and concentrated in vacuo. The residue was purified by C18 gel column chromatography (MeOH: H2O as an eluent). The product was dissolved in 3 mL MeOH: H2O: HCOOH (6:3:1), Pd(OH)2 (50% by weight) was added and the mixture was hydrogenated for overnight. The reaction mixture was filtered through Celite and concentrated in vacuo. The residue was purified by Bio-Gel P-2 (BIO-RAD) column chromatography using water as eluent. The product was lyophilized to get desired oligosaccharides 55 (0.002 g, 36%) as a white color powder. TLC: (n-BuOH: AcOH: H2O = 1/1/1, v/v): Rf = 0.32; 1H NMR (400 MHz, D2O): δ 5.15 (d, J = 4.2 Hz, 1H), 4.94 (s, 1H), 4.60 (m, 3H), 4.45 (q, 3H), 4.30 (s, 1H), 4.21 (d, J = 2.1 Hz, 1H), 4.13 (d, J = 2.0 Hz, 1H), 4.05-3.40 (m, 58H), 3.01 (t, 2H, linker), 2.10 (s, 3H, -Ac), 2.07 (s, 3H, -Ac), 2.06 (s, 3H, -Ac), 2.05 (s, 3H, -Ac), 1.76-1.58 (m, 4H, liner), 1.45-1.36 (m, 2H, linker), 1.21 (d, J = 6.5 Hz, 3H, Fuc-Me); 13C NMR (100 MHz, CHCl3): δ 174.6, 174.4, 102.9, 101.8, 101.0, 99.4, 99.1, 98.5, 96.8, 80.3, 79.6, 79.3, 78.4, 76.4, 75.3, 75.2, 74.7, 74.6, 74.5, 74.3, 73.5, 72.8, 72.4, 71.9, 71.0, 70.9, 70.0, 69.5, 69.4, 69.1, 68.5, 68.3, 67.7, 67.2, 66.7, 65.8, 61.4, 60.9, 59.6, 59.5, 55.6, 54.9, 54.8, 39.3, 28.0, 26.3, 22.3, 22.2, 22.0, 15.3; ESI-MS: m/z calcd for C73H125N5O50; 1871.7545 found 1872.7477 (M +H)+.
[00598] Chemical derivatization of sialylated module. Preparation of sialylated antennae is of particular importance due to the complexity associated with sialic acid chemistry. Having established the synthetic protocol for non-sialylated modules (Scheme S28), we turned our attention to sialylated module 22. The carboxylic acid functionality was esterified in presence of trimethylsilyl diazomethane without affecting free hydroxyl groups. Next, the peracetylation was performed using acetic anhydride and pyridine to afford S30a. The peracetylation step allows for purification of the oligosaccharide material before the removal of anomeric groups. At last, reducing end transformation was done to form anomeric fluoride donor S30b.
Figure imgf000267_0001
[00599] Scheme S28 | Reagents and Conditions. i, (1) Trimethylsilyl diazomethane, MeOH; (2) Ac2O, pyridine, RT, overnight; ii, (1) CAN, ACN: toluene: H2O, (2) DAST, CH2Cl2, -30 °C, 34% over 2 steps.
Figure imgf000267_0002
[00600] p-methoxyphenyl-O-[3,7,8,9-O-tetraacetyl-5-Acetamido-3,5-dideoxy-D-glycero-α- D-galacto-2-nonulopyrano-sylonate]-(2→6)-O-[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]- (1→4)-[3,6-O-diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-3,4,6-O-triacetyl- α-D-mannopyranoside (S28a): To a solution of compound 23 (30 mg, 0.031 mmol) in MeOH (3 mL) was added trimethylsilyl diazomethane (1M solution in hexane, 0.046 mL, 0.31 mmol). The resulting reaction mixture was stirred at RT for overnight. Complete consumption of starting material was confirmed by NMR and mass. The reaction mixture was concentrated to dryness and purified by C18 (eluent MeOH: H2O). TLC: (n-butanol: H2O: acetic acid = 2/1/1, v/v): Rf = 0.45; 1H NMR (400 MHz, MeOD): δ 7.14 (d, J = 9.5 Hz, 2H), 6.97 (d, J = 9.8 Hz, 2H), 5.50 (s, 1H), 4.68 (d, J = 8.5 Hz), 1H, 4.45 (d, J = 8.0 Hz, 1H), 4.36 (s, 1H), 4.20-3.90 (m, 10H), 3.84 (s, 3H), 3.76-3.58 (m, 17H), 3.51 (s, 3H), 2.66 (dd, J = 3.8 and 11.5 Hz, 1H), 2.00 (s, 3H), 1.96 (s, 3H), 1.60 (t, 1H); ESI-MS: m/z calcd for
C39H60N2O25; 942.3245 found 987.3033 (M + Na)+. [00601] A solution of methyl ester (0.025 mg, 0.025 mmol) in pyridine (2 mL) and acetic anhydride (1.5 mL) was stirred at rt for overnight. Reaction was then concentrated to dryness, dissolved in dicloromethane, extracted with saturated NaHCO3 solution, dried and concentrated. Product was purified by C18 column (MeOH: water eluent) to afford S28a (0.030 mg, 74%) as a white solid. TLC: (acetone: CH2Cl24/6, v/v): Rf = 0.42; 1H NMR (400 MHz, MeOD): δ 7.07 (d, J = 8.5 Hz, 2H), 6.88 (d, J = 8.9 Hz, 2H), 5.45 (s, 1H), 5.40 (d, J = 7.2 Hz, 1H), 5.36 (t, J = 10.3 Hz, 1H), 5.30 (d, J = 7.5 Hz, 1H), 5.28 (d, J = 7.0 Hz, 1H), 5.26 (s, 1H), 5.23 (s, 1H), 5.19 (d, J = 8.6 Hz, 1H), 5.17 (t, J = 10.3 Hz, 1H), 5.11-5.07 (m, 5H), 5.00-4.95 (m, 3H), 4.70 (dd, J = 4.2 & 7.8 Hz, 2H), 4.46-4.35 (m, 4H), 4.30-4.13 (m, 3H), 4.08-3.97 (m, 8H), 3.76 (s, 3H), 3.75 (s, 3H), 3.60-3.56 (m, 3H), 2.58 (dd, J = 4.2 & 8.5 Hz, 1H), 2.13 (s, 3H), 2.12 (s, 3H), 2.11 (s, 3H), 2.10 (s, 6H), 2.07 (s, 3H), 2.05 (s, 6H), 2.02 (s, 6H), 1.99 (s, 3H), 1.98 (s, 3H), 1.91 (s, 6H), 1.84 (t, J = 10.2 Hz, 1H); ESI-MS: m/z calcd for C63H84N2O37; 1461.3420 found 1486.4864 (M + 2H + Na)+.
Figure imgf000268_0001
[00602] p-methoxyphenyl-O-[3,7,8,9-O-tetraacetyl-5-Acetamido-3,5-dideoxy-D-glycero-α- D-galacto-2-nonulopyrano-sylonate]-(2→6)-O-[2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl]- (1→4)-[3,6-O-diacetyl-2-acetamido-2-deoxy-β-D-glucopyranosyl]-(1→2)-3,4,6-O-triacetyl- α-D-mannopyranosyl fluoride (S28b): Cerium ammonium nitrate (0.037 g, 0.065 mmol) was added to a solution of compound S28a (0.020 mg, 0.013 mmol) in 2 mL of acetonitrile: toluene: H2O (4:2:1). The resulting reaction mixture was stirred at RT for 3 h. The reaction was diluted with EtOAc (10 mL) and washed with H2O (10 x 2 mL) and brine (10 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The product was purified by C18 column chromatography (MeOH: H2O eluent) to afford 1-OH compound (11 mg). The residue (10 mg, 0.007 mmol) was dissolved in CH2Cl2 (5 mL) at -30 °C. Then, DAST (3 µL, 0.021 mmol) was added slowly, and the resulting reaction mixture was stirred for 1 h. When TLC (acetone: CH2Cl2, 4/6) indicated formation of product with consumption of starting material, the reaction was quenched with aq. NaHCO3. The filtrate was washed with aqueous NaHCO3 (2 x 5 mL) and brine (5 mL) solution. The organic layer was dried over Na2SO4 and concentrated in vacuo. The residue was purified by C18 column
chromatography (MeOH: H2O eluent) to afford S30b (0.007 g, 38% over 2 steps). TLC (acetone: CH2Cl2 = 6/6, v/v), Rf = 0.24; 1H NMR (400 MHz, CHCl3): δ 5.99 (d, J = 10.2 Hz, 1H), 5.50 (d, J = 52.2 Hz, 1H), 5.39 (d, J = 10.3 Hz, 1H), 5.33-5.17 (m, 7H), 4.87-4.81 (m, 2H), 4.61 (d, J = 10.2 Hz, 1H), 4.52 (d, J = 10.3 Hz, 1H), 4.40-4026 (m, 5H), 4.21-3.83 (m, 4H), 3.70 (s, 3H), 3.49-3.47 (m, 2H), 2.54 (dd, J = 3.8 & 8.1 Hz, 1H), 2.19 (s, 6H), 2.17 (s, 6H), 2.14 (s, 6H), 2.10 (s, 3H), 2.05 (s, 6H), 2.02 (s, 6H), 1.98 (s, 3H), 1.97 (s, 6H), 1.23 (t, J = 10.1Hz, 1H); ESI-MS: m/z calcd for C56H77FN2O35; 1357.2094 found 1339.3978 (M + Na)+.
Glycan Array Analysis
Microarray Fabrication
[00603] a) Fabrication of N-hydroxy succinimide-coated glass slide: All monovalent glycans (G1-33) were prepared in 10 mM concentration individually and served as mother solutions which are to be diluted with printing buffer to prepare a working solution. Microarrays were printed (BioDot Cartesian Technologies) by robotic pin (SMP3: TeleChem International) deposition of ~ 0.6 nL of 100 µM concentration of amine-containing glycans in printing buffer from a 384 well plate onto NHS-coated glass slides. The printed slides were allowed to react in an atmosphere of 80% humidity for an hour followed by desiccation overnight. These slides were designed for 16 grids in one slide, and stored at room temperature in a desiccator prior to use. Before the binding assay, these slides were blocked with blocking solution for 3 h. The slides were then washed with PBST-BSA buffer prior to use. Unless otherwise stated, reagents were obtained from commercial suppliers and used without purification. All aqueous solutions were prepared from distilled de-ionized water filtered with a Milli-Q purification system and sterile filtered through a 0.2 µm filter. Buffers used in the experiment include the printing buffer (pH 8.5, 300 mM phosphate buffer containing 0.05% (v/v) Tween-20), the blocking buffer (superblock blocking buffer in PBS, Pierce), the washing buffer (PBST buffer; PBS and 0.05% Tween-20) and the binding buffer (PBST-BSA Buffer; PBST buffer and 3% BSA). Printing buffer, blocking buffer, and binding buffer were prepared freshly before use.
[00604] b) Fabrication of aluminum oxide coated glass slide. The aluminum oxide glass substrate provides advantages for being able to be assessed by both mass spectrometry and fluorescence scanning. In addition, the fluorescence intensity of sugar-protein binding on the substrates was found to be more sensitive than that on transparent glass slide15. There are many reports describing the surface of micron to nano pore structures of anodized aluminum oxide. However, only a few articles have mentioned the initial planar layer of aluminum oxide16 during the treatment of surface anodization. In the development of AAO glass substrate, a computer experimental design program (Design Expert 8.0) has been used to optimize the planar layer of surface anodized aluminum oxide to be best used in glycan microarray17.
Figure imgf000271_0001
Figure S4 | Schematic drawing of the fabrication of anodized aluminum oxide (AAO) glass substrate.
[00605] As shown in Figure S4, approximately a larger of 300 nm aluminum coated on glass slide (1 x 75.5 x 24.5 mm) was fabricated using E-Beam VDP coater by The Thin Film Technology Division, Instrument Technology Research Center at National Applied Research Laboratories, (Hsinchu Science Park, Hsinchu, Taiwan, R.O.C.). The slide after Al-coating was immediately packed (one slide per container) and vacuum sealed in air-tight laminated foil pouches until the moment for surface anodization. Surface anodization of the aluminum coated glass slide has been conducted in-house via electrochemical reaction in a 0.3 M oxalic acid aqueous solution in a 4 °C chamber. The anodization reaction was controlled by voltage and reaction time. Under proper reaction conditions, a layer of approximately 50 to 65 nm (in thickness) of smooth anodized aluminum oxide (AAO) can be grown consistently on top of aluminum coated glass slide. Unlike the conventional anodic aluminum oxide surface with pores, as the AFM picture shown in Figure S5A, we have developed a smooth AAO glass substrate with Rsm surface roughness (2.3 nm) similar to the surface of glass slide (< 3 nm). The cross section picture of a typical AAO glass substrate is shown in Figure S5B. To obtain the optimized AAO glass substrate with its physical properties shown in Figure S5, the detail experiment using computer program generated factorial design and response surface methodology has been conducted and will be reported in a separate article.
Figure imgf000272_0001
Figure S5 | (A) AFM picture– Roughness Analysis of the surface. Img. Rms (Rq) 2.319 nm and (B) Cross Section SEM picture of the AAO Glass Substrate.
[00606] Surface Comparison of AAO Glass Substrate vs. NHS-Activated Glass Slide S
[00607] NHS-glass slide has been widely used for glycan microarray in our and other groups. The amide formation of the NHS functional group with the amine of sugar derivative was taken place on the surface. Its first chemical reaction was to covalently bond to the carboxyl group of the functionalized glass surface. The AAO glass substrate contains a layer of stable polymer network of amorphous aluminum oxide on the surface which is ready for the chemical reaction with the phosphonic acid tail of glycan derivative to form a phosphonate. Interface reaction of phosphonic acid on metal oxides, either aluminum oxide or titanium oxide, is spontaneous and the resulting array is more homogeneous, and density and distribution can be easily controlled compared to the reactions on NHS slide. To identify the reactive site available for interface covalent bonding, Cy5-phosphonic acid and Cy5-amine have been used for microarray on the surfaces directly. These dyes (Figure S6) have been synthesized in-house starting from Cy5-NHS ester (Lumiprobe Corp. Item No.63020).
Figure imgf000273_0001
Figure S6 | Structures of Cy5-phosphonic acid linker and Cy5-amine linker
[00608] The dyes, Cy5-phosphonic acid and Cy5-amine, were dissolved in a 7:3 ratio of ethylene glycol/water mixtures (1 mM) with pH adjustment to 6 and 8.5 respectively. The arrayed slides were washed thoroughly with a mixture of 5% methanol in water, spin-dried before subjecting for GenePix (4300A) Scanning. Figure S7 shows the microarray pictures of Cy5-phosphonic acid on AAO glass substrate (Figure S7A), Cy5-amine on NHS-glass slide (Figure S7B) and their 20 spots average fluorescence intensity (Figure S7C). The representative confocal microscope pictures of these arrayed spots are given in Figure S8. Higher loading capacity and more uniformly distributed Cy5-molecules have been observed similarly to those which have been seen usually in the glycan microarray and sugar/protein binding.
Figure imgf000274_0001
Figure S7 | GenePix Scanning (at PMT 450) of 1 mM of (A) Cy5-phosphonic Acid on AAO glass substrate (B) Cy5-Amine on NHS glass slide, and (C) their averaged 20 spots fluorescence intensity.
Figure imgf000274_0002
Figure S8 | Representative Confocal Microscopes pictures Cy5-phosphonic Acid, and Cy5- Amine on AAO glass substrate and NHS glass slide. Selective 900 μm2 area within the spots.
[00609] Surface uniformity comparison of ACG and NHS slide using confocal microscope
[00610] To evaluate the density and uniformity of glycan array on ACG and NHS activated glass slide, we used the mannose monosaccharide formed glycan array as a model. A mannose solution of 100 µM was used in arraying, and a solution of ConA488 of 50 µg/mL was used in sugar/protein binding. The images of ConA488/mannose binding observed from confocal microscope further confirmed that the AAO glass substrate has denser and more uniformly distributed covalently bonded sugars. Figure S9 shows the images observed from Confocal Microscope (Leica SP5) of ConA488/mannose binding on AAO Glass Substrate vs. NHS Glass Slide.
Figure imgf000275_0001
Figure S9 | Confocal Microscope of ConA488/Mannose binding on AAO glass Substrate vs. NHS-Glass Slide.
[00611] Atomic force microscopy image of sugar distribution on aluminum-oxide coated glass slide, and NHS coated glass slide suggest that the AAO glass substrate (Figure S10a) provides more uniform distribution of covalently bonded sugars than that of NHS glass slide (Figure S10a). Particle counts of these images were obtained by counting the particles over the height of one half width distribution of the maximum numbers of particle height.
Mannose derivatives can only covalently bond on the slides where the activated functional groups were available on the surface. Regardless of differences in Rms of the glass base materials, the AAO glass substrate provides more homogeneous distribution than that of NHS glass slide.
Figure imgf000276_0001
Figure S10 | Atomic force microscopy image showing sugar distribution on a) aluminum- oxide coated glass slide, and b) NHS coated glass slide
[00612] Antibody binding assay
[00613] Antibodies PG9, PG16 and PGTs 141-145 were diluted by binding buffer to 100 µg/mL prior to use. DyLight649-conjugated Donkey Anti-Human IgG antibody was then pre-complexed with primary antibodies. The final concentration of the precomplexed solution was adjusted to 50 µg/mL with binding buffer. The printed glass slide was assembled into FAST® frame slide holder (Whatman®), 80 µL of precomplexed antibody solution were then applied to each well accordingly. The antibodies binding process was maintained in 4 °C with gentle shaking and then antibody solutions were carefully pipetted out after 6 hours incubation. The glass slide was gently washed by 100 µL PBST washing buffer and then spin-dried for 3 minutes.
[00614] Image processing and data analysis
[00615] The slide was scanned at 635 nm with a microarray fluorescence chip reader (GenePix® 4300A, Molecular Devices Corporation). Scanned images were analyzed with GenePix Pro 6.0 analysis software (Molecular Devices Corporation,). The image resolution was set to 5 µm per pixel. Spots were defined as circular features with defined diameter of 100 µm. The values of total intensity were chosen for data processing, performed with Graphpad Prism® 6.0. The intensities was calculated and averaged. Error bars represent the standard deviation for all data points reported.
[00616] Analyzing glycan binding specificity of HIV-1 bNAbs on NHS-coated glass slide
[00617] The slide for the study of PG9, PG16 and PGTs141-145 was prepared by printing glycans G1-33 (Figure S11) on the N-hydroxysuccinimide coated surface through covalent bond formation. Slide images obtained by fluorescent scan after secondary antibody incubation.
Figure imgf000277_0001
Figure S11 | Schematic representation of N-glycans printed on NHS coated glass slide.
[00618] Having incorporated diverse HIV-1 gp120 related N-glycans in our array, we next proceed to characterize binding behavior of PG16 to those glycans. Our results are consistent with our previously reported data, where, the PG16 binding is proportional to α 2,6-Neu5Ac count at the termini (Figure S12). A short conclusion from our study is presence of di-sialylated antennae in defined orientation is deterministic of binding in PG16 binding pocket.
Figure imgf000278_0001
Figure S12. Binding behavior of PG16 using NHS-coated glass slide. Bindings of PG16 to panel of N-glycans represented in bar chart.
[00619] Binding of defined set of glycans binding to antibodies PG9 and PGTs141-45. We screened PG9 and PGTs141-145 on our NHS-coated glass slide array.
[00620] Figure S13. Binding behavior of PG9 using NHS-coated glass slide.
[00621] Figure S14. Binding behavior of PGTs 141-143 using NHS-coated glass slide. Antibody concentrations used here are 25 µg/mL.
[00622] Figure S15. Binding behavior of PGTs14-145 using NHS-coated glass slide.
Antibody concentrations used here are 25 µg/mL.
[00623] We observed a low level binding for antibodies PG9 (Figure. S13) and PGTs 141- 145 (Figure. S14-15) towards any of the glycans printed on array.
[00624] Analyzing glycan binding specificity of HIV-1 bNAbs onACG slide.
[00625] Having demonstrated the applicability of ACG slide over NHS-coated slide in terms of glycan density and enhancement in signal intensity, we printed glycan glycans I-XI on ACG array using phosphonate chemistry (Figure S17). The binding specificities of PGTs141-144 are shown below.
Figure imgf000279_0001
Figure S17. Cartoon represents glycans printed on ACG array. The structure of linker is shown on the upper left corner.
[00626] The binding specificities of PGTs141-144 are shown in Figure S18. However, we could not find the binding for PGT145 on ACG array, most probably because of its weak glycan binding affinity.
Figure imgf000279_0002
Figure S18. Bindings of PGTs 141-144 towards panel of N-glycans on ACG array is shown in bar chart.
[00627] Determination of surface dissociation constants (KD.surf) on ACG slide
[00628] The aluminum oxide coated glass slides for the determination of dissociation constants were spotted with 100 and 50 µM concentrations of glycans Man5GlcNAc2 (V), hybrid type (XI), bi-antennary complex type (XII), V+XI (1:1 mole ratio), V+XII, and XI+XII. Antibody PG16 was serially diluted to 3.32, 1.66, 0.833, 0.415, 0.207, 0.103, 0.051 and 0.025 µM with 3% BSΑ-PBST buffer. DyLight649-conjugated Donkey Anti-Human IgG antibody was pre-complexed with primary antibody PG16 (1:1 by weight). The pre- complexed solution (100 μL) was applied to each well and incubated at 4 °C for 6 h in the dark. Finally, slides were washed with PBST, spin dried and scanned at 450 nm with a microarray fluorescence chip reader. Scanned images were analyzed with GenePix Pro 6.0 analysis software. The signal intensities for binding of PG16 to Man5GlcNAc2 (V) and mixture of V+XI (1:1 mole ratio) were too weak to determine the KD. The binding curves for the rest of samples printed on array are shown in Figure S19 and KD values are summarized in Table S2.
[00629] In the case of PG9, because of its very weak glycan binding affinity, we were not able to achieve the signal saturation to measure the binding constants, however, increasing PG9 concentration to 700 μg/mL resulted in a precipitation on array surface.
Figure imgf000280_0001
Figure imgf000281_0001
Figure S19. Antibody PG16 binding curves observed for glycans X, XI and mixtures V+XI and X+XII at 100 µM concentration. The curves were obtained by using DyLight649- conjugated donkey anti-Human IgG secondary antibody.
[00630] Table S2. KD, surf (µM) values of antibody PG16 and glycans X, XI and mixtures V+XI and X+XI.
Figure imgf000281_0002
ADDITIONAL EXAMPLES
[00631] Additional Examples are attached as a separate document, labeled P3-1 through P3-7.
[00632] Additional Examples: (P3-1)
Compound 42, is a transformer of mixed compound 4 and compound 20, therein, it is also recognized and bound by anti HIV-1 broadly neutralizing monoclonal antibodies (bnMAb) with binding and recognition the mixture of compound 4 and compound 20, e.g. PG9 and PG16
[00633] Additional Examples: (P3-2)
Schematic representation of N-glycans printed on NHS coated glass slide
[00634] Additional Examples: (P3-3)
Synthesis of Compound 42
[00635] Additional Examples: (P3-4)
[00636] General Exemplary Procedures for the synthesis of Hybrid Glycans with Man3/Man5 Glycan at the 3-Arm and Complexed Glycan at the 6-Arm
[00637] Additional Examples: (P3-5)
[00638] General Exemplary Procedures for the synthesis of Hybrid Glycans with Man3/Man5 Glycan at the 6-Arm and Complexed Glycan at the 3-Arm
[00639] Additional Examples: (P3-6)
[00640] Exemplary Hybrid Glycans via synthesis
[00641] Additional Examples: (P3-7)
[00642] Exemplary Hybrid Glycans via synthesis
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Claims

WHAT IS CLAIMED IS
1. An orthogonally protected Manβ1–4GlcNAcβ1–4GlcNAcβ1 core trisaccharide having the formula (I)
Figure imgf000290_0001
wherein each of R1, R2, R3, R4, R5, R6, R7, and R8 is independently selected from the group consisting of an orthogonal or a permanent protecting groups; wherein, each of the orthogonal protecting groups at R6 is preferably selected from the group consisting of para- methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), levulinoyl (Lev), benzoyl (Bz), allyl ether (allyl), and silyl ethers; and R7 and R8 are fused to form a benzylidene ring which can be cleaved to form either 4-OH and/or 6-OH glycan structures;
each of R2, R3, R4, and R5 is independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac);
R1 is a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac); or a protected fucoside residue connected via α 1,6 linkage;
X is–OR9; wherein R9 is–H or optionally substituted C3-C10 alkyls chains terminated with the group consisting of–N3 and NR10; and R10 is–H or benzyl (Bn) or carbobenzoyl (Cbz);
Y and Z are–NHR11; and R11 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (alloc), [2,2,2- trichloroethoxycarbonyl] (troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) and tert-butoxycarbonyl (Boc). 2. A D1 and D2/D3 arm module having the general formula (II)
Figure imgf000291_0001
wherein, each of R1, R2, R3, and R4 is–H or a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
Figure imgf000291_0002
wherein, Each of R5, R6, R7, and R8 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz);
each of R9 and R10 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or a protected fucoside residue connected via α 1,3 linkage to GlcNAc and/or α 1,2 linkage to galactose;
R11 is–H, Me (methyl) or Et (ethyl); R12 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or protected Neu5Ac residue connected via α 2,6 linkage;
R13 is–H or independently a permanent protecting group that is stable under conditions used to remove the orthogonal protecting groups and is preferably benzyl (Bn) or acetyl (Ac) or benzoyl (Bz), or independently selected from
Figure imgf000292_0001
X is–OR14 or–SR15 or leaving group;
wherein, R14 is H, alkyl, alkenyl, alkynyl, aryl or substituted aryl; a protecting group such as a silyl or substituted silyl, preferably thexyldimethylsilyl (TDS), t-butyldimethylsilyl (TBS), t- butyldiphenyl silyl (TBDPS), triisopropylsilyl (TIPS), trimethylsilyl (TMS), or triethylsilyl (TES); methyl (Me), acetyl (Ac), benzyl (Bn), 2-naphthylmethyl (nap) or 1- naphthylmethyl (1-Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), allyl ether (allyl), or an anomeric leaving group such as trichloroacetimidate -C(NH)-CCl3, phenyltrifluoroacetimidate -C(NPh)-CF3, trifluoroacetimidate -C(NH)-CF3; thioalkyl, thiophenyl, and more preferably fluoride;
R15 is H, alkyl, aryl, or substituted aryl, preferably methyl, ethyl, phenyl, tosyl, or tolyl;
Y is–NHR16; and R16 is preferably selected from the group consisting of 9- fluorenylmethoxycarbonyl (Fmoc), allyloxycarbonyl (Alloc), [2,2,
2- Trichloroethoxycarbonyl] (Troc), acetyl (Ac), phthalimido (Phth), carbobenzyloxy (Cbz) and tert-butoxycarbonyl (Boc);
wherein“D1 and D2/D3 arm modules” refers to N-glycans.
3. A method for synthesizing diverse glycans suitable for generating glycan arrays wherein the method comprises:
a) generating orthogonally protected core trisaccharide of claim 1 and D1 and D2/D3 arm modules of claim 2,
b) performing Stereo- and regio-selective glycosylation of D1 and D2/D3 arm modules of claim 2 to 3-O or/and 6-O positions of orthogonally protected core trisaccharide of claim 1,
c) Unmasking or removal of protecting groups to obtain the high mannose, hybrid and bi-, tri- and tetraantennary complex-type glycans, and
d) performing enzymatic sialylation to generate a library of sialylated glycans.
4. A method of preparation of the D1 and D2/D3 arm modules of claim 2, wherein the method comprises chemical and chemo-enzymatic synthesis.
5. The D1 and D2/D3 arm modules of claim 2, wherein the modules are selected from the group consisting of
Figure imgf000294_0001
6. The method of claim 4, further comprising:
stepwise enzymatic extension of chemically synthesized acceptors substrates having formula (III)
Figure imgf000294_0002
wherein,
each of R1 and R2 is independently selected from–H or acetyl (Ac) or benzoyl (Bz); X is–OR3 and R3 is H, benzyl (Bn), 2-naphthylmethyl (Nap), 1-naphthylmethyl (1- Nap); para-methoxy benzyl ether (PMB), methoxy phenyl ether (PMP), or allyl ether (allyl).
7. The method of claim 6, wherein the enzymes are independently selected from the group consisting of β (1→4) Galactosyltransferase, α (1→3) Fucosyltransferase, α (1→2) Fucosyltransferase, β (1→3) N-acetyl glucosamine transferase, α (2→3) sialyltransferase, and α (2→6) sialyltransferase.
8. An array of carbohydrates moieties prepared according to the method of claim 3, the array comprising:
a plurality of glycans wherein each glycan moiety is deposited at a discrete location on a substrate, wherein the diverse glycans comprises homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types.
9. The array of claim 8, wherein the glycans comprise homo- and/or mixed N-glycans of high-mannose-, hybrid-, and complex- types prepared by the methods of any one of claims 3, 4, 6, and 7.
10. A method of detecting hetero-glycan binding behavior comprising contacting the array of claim 8, with one or a plurality of hetero-glycans.
11. The array of claim 9, wherein the glycans further comprise the glycans recognized by broadly neutralizing HIV-1 antibodies.
12. The array of claim 8, wherein the substrate comprises an aluminum oxide-coated glass (ACG) surface.
13. The array of any one of claims 8 or 11, wherein the glycans comprise one or more of the compounds G1-G33 set forth in Figure S11 and/or any one or more of the compounds I- XI set forth in Figure S17.
14. The array of claim 9, wherein the glycans can include or exclude one or more of the compounds G1-G33 set forth in Figure S11 and include or exclude any one or more of the compounds I-XI set forth in Figure S17.
15. A method for generating vaccine targets comprising:
screening and identifying optimal cell surface glycans recognized by neutralizing HIV-1 antibodies wherein the method further comprising contacting the HIV antibodies with the array of any one of claims 8, 9, 11, 12, or 13.
16. The array of claim 8, wherein the substrate is selected from a surface, a solid surface, a non-transparent solid, a solid transparent to selected wavelengths of visible or non-visible light, a particle, a microbubble, or a bead.
17. The array of claim 8, wherein the plurality of N-glycans are coated on the substrate or are adhered to the substrate by van der Waals interactions or by hydrophobic interactions.
18. An array of N-glycans immobilized on a substrate wherein the array is fabricated by a method comprising:
(a) providing a substrate;
(b) attaching the N-glycan via a linker to the substrate; and
(c) immobilizing a plurality of N-glycan moieties at discrete locations on the surface of the substrate.
19. A method of characterizing the array of claim 18, comprising contacting the immobilized N-glycan moieties with a labeled antibody to the glycans, forming complexes between the antibody and the glycan, and detecting the complexes.
20. The method of claim 19, wherein the labeled antibody comprises a label comprising an enzyme, fluorescent label, a chemiluminescent label, or a nanoparticle label.
21. A method of detecting HIV antibodies, the method comprising:
(a) providing the array of claim 18;
(b) contacting the array with HIV antibodies;
(c) forming a complex between the HIV antibodies and the glycans on the array; (d) contacting the HIV antibody-glycan array complex with a label; and
(e) detecting the label.
22. The method of claim 21, wherein the label is a labeled antibody further comprising an enzyme, fluorophore, chemiluminescent moiety, or a nanoparticle.
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