Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes

To explore the molecular basis of antigen recognition by germline antibodies, we have determined to high resolution the structures of the near-germline monoclonal antibody S25-2 in complex with seven distinct carbohydrate antigens based on the bacterial sugar 3-deoxy-α-d-manno-oct-2-ulosonic acid (Kdo). In contrast to previous findings, the inherited germline Kdo monosaccharide binding site is not restricted to this bacterial sugar but is able to accommodate an array of substitutions and chemical modifications of Kdo, including naturally occurring antigens containing the related monosaccharide d-glycero-α-d-talo-oct-2-ulosonic acid as well as nonterminal Kdo residues. However, we show by surface plasmon resonance and ELISA how antibody S25-2 specificity is so dependent on the context in which the antigen is presented that a free disaccharide displays strong binding while the same lipid-A-bound disaccharide does not bind. These structures provide insight into how inherited germline genes code for immunoglobulins of limited flexibility that are capable of binding a range of epitopes from which affinity-matured antibodies are generated.     

Synthese von O-(3-desoxy-α-d-manno-2-octulopyranosylonsäure)-(2→4)-O-(3-desoxy-α-d-manno-2-octulopyranosylonsäure)- (2→6)-O-(2-amino-2-desoxy-β-d-glucopyranosyl)-(1→6)-2-amino-2-desoxy-d-glucopyranose

Benzyl-3-O-benzyl-2-benzyloxycarbonylamino-6-O-[2-benzyloxycarbonyl-amino-2-deoxy-3,4-O-(tetraisopropyldisiloxane-1,3-diyl)- β-d-glucopyranosyl]-2-deoxy-α-d-glucopyranoside was coupled with methyl (4,5,7,8-tetra-O-acetyl-3-deoxy-α-d-manno-2-octulopyranosyl bromide)onate (13) to yield the α-glycosidically linked trisaccharide. After deacetylation and selective introduction of a second 7′,8′-O-tetraisopropyldisiloxane group, a further glycosidation reaction with 13 led regioselectively to the tetrasaccharide benzyl O-[methyl (4,5,7,8-tetra-O-acetyl-3-deoxy-α-d-manno-2-octulopyranosyl)onate]-(2→4)-O-{methyl [3-deoxy-7,8-O-(tetraisopropyldisiloxane-1,3-diyl)-α-d-manno-2-octulopyranosyl]-onate}-(2→6)-O- [2-benzyloxycarbonylamino-2-deoxy-3,4-O-(tetraisopropyldisiloxane-1,3-diyl)-β-d-glucopyranosyl]- (1→6)-3-O-benzyl-2-benzyloxycarbonyl-amino-2-deoxy-α-d-glucopyranoside. A series of deblocking steps gave O-(3-deoxy-α-d-manno-2-octulopyranosylonic acid)-(2→4)-O-(3-deoxy-α-d-manno-2-octulopyranosylonic acid)- (2→6)-O-(2-amino-2-deoxy-β-d-glucopyranosyl)-(1→6)-2-amino-2-deoxy-d-glucopyranose which was identical with a tetrasaccharide that had been isolated by hydrazinolysis of the lipopolysaccharide from Salmonella minnesota R 595. Hence, synthetic proof is provided for the linkages in this part of the inner core region of lipopolysaccharides.     

The reactions of 3-deoxy-d-manno-oct-2-ulosonic acid (KDO) in dilute acid

On heating in dilute acid, 3-deoxy-d-manno-oct-2-ulosonic acid (KDO) is converted into 2,7-anhydro-3-deoxy-α-d-manno-2-octulofuranosonic acid and 5-(d-erythro-1,2,3-trihydropropyl)-2-furoic acid. The former is unreactive to periodic acid-thiobarbituric acid and to semicarbazide, and its formation explains the depressed estimates of KDO in lipopolysaccharides. Formation of the furoic acid can lead to high estimates using the semicarbazide assay. Neither product can be formed from 5-O-glycosyl-KDO.     

Synthesis of 2-amino-2-deoxy- and 3-amino-3-deoxy-α-d-mannopyranosyl α-d-mannopyranoside by sequential osmylations of a dienic disaccharide

Partial oxyamination of 4,6-di-O-acetyl-2,3-dideoxy-α-d-erythro-hex-2-enopyranosyl 4,6-di-O-acetyl-2,3-dideoxy-α-d-erythro-hex-2-enopyranoside with chloramine-T and osmium tetraoxide gave 4,6-di-O-acetyl-2-deoxy-2-(p-toluene-sulfonamido)-α-d-mannopyranosyl 4,6-di-O-acetyl-2,3-dideoxy-α-d-erythro-hex-2-enopyranoside and its 3-deoxy-3-(p-toluenesulfonamido) regioisomer, each in 18–19% isolated yield. Osmium tetraoxide-catalyzed cis-hydroxylation of the remaining alkenic residue in these products led in high yields to the corresponding triols having the α-d-manno, α-d-manno configuration. These were N-desulfonylated (and simultaneously O-deacetylated) by the action of sodium in liquid ammonia to furnish 2-amino-2-deoxy-α-d-mannopyranosyl α-d-mannopyranoside and 3-amino-3-deoxy-α-d-mannopyranosyl α-d-mannopyranoside as new, trehalose-type amino sugars.     

Further applications of selective displacements in an unsymmetrical ditriflate. Synthesis of new triamino and tetraamino disaccharides of the trehalose type

Although the known ring-opening with sodium azide in 2,3-anhydro-4,6-O-benzylidene-α-d-allopyranosyl 2,3-anhydro-4,6-O-benzylidene-α-d-allopyranoside gave mainly symmetrical 2-azido-4,6-O-benzylidene-2-deoxy-α-d-allopyranosyl 2-azido-4,6-O-benzylidene-2-deoxy-α-d-allopyranoside (2), the unsymmetrical 2,3′-diazido isomer 3 having the α-d-altro, α-d-gluco configuration was shown to be a second product that can be conveniently isolated on a preparative scale. The ditriflate 4 derived from 3 was subjected to regioselective displacement in the altro moiety with sodium azide, followed by displacement with sodium benzoate in the gluco moiety, to give a 2,3,3′-triazide having the α-d-manno, α-d-manno configuration. Alternatively, 4 was subjected to displacement first with benzoate and then with azide, thus providing the regioisomeric 2,3,2′-triazide of the same configuration. The ditriflate obtained from 2 furnished the corresponding 2,3,2′,3′-tetraazido derivative. Minor proportions of elimination products also arose in these reactions. The protected azido sugars were converted by standard methods into the 2,3,2′- and 2,3,3′-triamino derivatives and the 2,3,2′,3′-tetraamino derivative of α-d-mannopyranosyl α-d-mannopyranoside.     

Syntheses of repeating units of Escherichia coli capsular polysaccharides containing d-ribose and 3-deoxy-d-manno-2-octulosonic acid (KDO)

The oligosaccharides, sodium (methyl 3-deoxy-7-O-β-d-ribofuranosyl-β-d-manno-2-octulopyranosid)onate, methyl 2-O-β-d-ribofuranosyl-β-d-ribofuranoside, and the anomeric sodium [methyl 3-deoxy-7-O-(2-O-β-d-ribofuranosyl-β-d-ribofuranosyl)-α- and -β-d-manno-2-octulopyranosid]onate were prepared from 1-O-acetyl-2,3,5-tri-O-benzoyl-β-d-ribofuranose and the anomeric methyl (methyl 8-O-benzyl-4,5-O-carbonyl-3-deoxy-α- and -β-d-manno-2-octulopyranosid)onate in high purity and in acceptable over-all yields. They constitute a first series of model compounds for spectroscopic and immunochemical studies of the capsular polysaccharides from Escherichia coli strains LP 1092 and K 23. The essential, interglycosidic linkages [β-d-Ribf-(1→7)-α- or -β-d-dOclA, and β-d-Ribf-(1→2)-β-d-Ribf] were formed by a modification of the silver triflate procedure using appropriate d-ribofuranosyl bromide derivatives. The constitutional and configurational assignments were based on the 250-MHz ¹H-n.m.r.-spectra of protected derivatives of the oligosaccharides.     

Synthesis of the trisaccharide repeating unit related to Klebsiella 012 serotype

Synthesis of the trisaccharide, allyl α-l-rhamnopyranosyl-(1→3)-2-acetamido-2-deoxy-β-d-glucopyranosyl-(1→4)-α-l-rhamnopyranoside related to O-chain glycans isolated from the deaminated LPSs of Klebsiella pneumoniae serotype 012, was achieved through condensation of suitably synthesized disaccharide, allyl 4,6-O-benzylidene-2-deoxy-2-phthalimido-β-d-glucopyranosyl-(1→4)-2,3-di-O-benzoyl-α-l-rhamnopyranoside and donor, ethyl 2,3,4-tri-O-acetyl-1-thio α-l-rhamnopyranoside starting from l-rhamnose and d-glucosamine hydrochloride. The trisaccharide can be utilized for the synthesis of neoglycoconjugates for use as a synthetic vaccine by coupling it with a suitable protein after deprotection. Various regio- and stereoselective protecting group strategies have been carefully considered, as protecting groups can influence the reactivity of the electrophile and nucleophile in glycosylation reactions on the basis of steric and electronic requirements.     

Artificial carbohydrate antigens: the synthesis of a tetrasaccharide hapten,a Shigella flexneri O-antigen repeating unit

The 8-methoxycarbonyloctyl glycoside of the tetrasaccharide hapten, O-α-l-rhamnopyranosyl-(1→2)-O-α-l-rhamnopyranosyl-(1→3)-O-α-l-rhamnopyranosyl-(1→ 3)-2-acetamido-2-deoxy-β-d-glucopyranoside and the trisaccharide glycoside 8-methoxycarbonyloctyl O-α-l-rhamnopyranosyl-(1→3)-O-α-l-rhamnopyr-anosyl-(1→3)-2-acetamido-2-deoxy-β-d-glucopyranoside were synthesized by sequential Koenigs-Knorr reactions from monosaccharide units. The tetrasaccharide represents the complete skeletal repeating unit of Shigella flexneri serogroup Y lipopolysaccharide. Both oligosaccharide haptens are functionalized for covalent attachment to proteins, cell surfaces, and solid supports. ¹H-N.m.r. evidence for the conformations of these oligosaccharides in solution is presented and shown to be consistent with predictions based on the exo-anomeric effect     

Synthesis of phosphorylated 3,4-branched trisaccharides corresponding to LPS inner core structures of Neisseria meningitidis and Haemophilus influenzae

2-(N-Benzyloxycarbonyl)aminoethyl 7-O-acetyl-6-O-allyl-2-O-benzoyl-4-O-benzyl-3-O-chloroacetyl-l-glycero-α-d-manno-heptopyranosyl-(1→3)-[2,3,4,6-tetra-O-benzoyl-β-d-glucopyranosyl-(1→4)]-6,7-di-O-acetyl-2-O-benzyl-l-glycero-α-d-manno-heptopyranoside, a spacer-equipped protected derivative of the common 3,4-branched diheptoside trisaccharide structure of the lipopolysaccharide core of Neisseria meningitidis and Haemophilus influenzae has been synthesized. The protecting group pattern installed allows regioselective introduction of phosphoethanolamine residues in the 3- and 6-position of the second heptose unit in accordance with native structures. From this intermediate the 3-and 6-monophosphoethanolamine as well as the non-phosphorylated deprotected trisaccharides have been synthesized to be used in evaluation of antibody binding specificity and in investigation of the substrate specificity of glycosyl transferases involved in the biosynthesis of LPS core structures.     

Reaction of organocuprate reagents with protected 1,2-anhydro sugars. Stereocontrolled synthesis of 2-deoxy-C-glycosyl compounds

The reaction of protected 1,2-anhydro-α-d-gluco- and β-d-manno-pyranoses with alkyl and phenyl organocuprates afforded the corresponding C-glycosyl compounds in acceptable to high yield. Complete stereocontrol was obtained, leading respectively to the β-d or the α-d anomer. With the perbenzylated manno derivative, deoxygenation at C-2 was achieved in high yield, affording 2-deoxy-α-d-C-glycosyl compounds.     

The structure and properties of the products of reaction between 3,4,6-tri-O-acetyl-2-deoxy-2-nitroso-α-d-galactopyranosyl chloride and pyrazole

Dimeric 3,4,6-tri-O-acetyl-2-deoxy-2-nitro-α-d-galactopyranosyl chloride reacts with pyrazole in acetonitrile to give 1-(3,4,6-tri-O-acetyl-2-deoxy-2-hydroxyimino-α-d-lyxo-, -β-d-lyxo-, and -β-d-xylo-hexopyranosyl)pyrazole. The stereospecificity of the reaction depends on the temperature and its duration. Transformations of the type α-d-lyxo-←β-d-lyxoα β-d-xylo have been observed. The condensation products were modified at C-2 or C-3. The following derivatives have thus been obtained: 1-(α-d-galacto-, 2-acetamido-2-deoxy-α-d-galacto-, -α-d-talo-, and -α-d-xylo-hexo-pyranosyl)pyrazole, (Z)- and (E)-1-(3-azido-2,3-dideoxy-2-hydroxyimino-α- and -β-d-lyxo- and -α-d-xylo-hexopyranosyl)pyrazole, 1-(3-acetamido-2-acetoxyimino-4,6-di-O-acetyl-2,3-dideoxy-α- and -β-d-lyxo-hexopyranosyl)pyrazole, as well as (Z)- and (E)-1-(2,3-dideoxy-2-hydroxyimino-α-d-threo-hexopyranosyl)pyrazoles.     

Synthèse des l-fucose et l-(3-2H)fucose à partir du d-mannose

Oxidation with the dimethyl sulfoxide-acetic anhydride reagent of methyl 2-O-acetyl-4,6-O-benzylidene-α-d-mannopyranoside, obtained in quantitative yield from the corresponding 4,6-benzylidene acetal by stereoselective opening of a 2,3-orthoester, led in good yield to methyl 2-O-acetyl-4,6-O-benzylidene-α-d-arabino-hexopyranosid-3-ulose, which was reduced with either sodium borohydride or sodium borodeuteride into a methyl 4,6-O-benzylidene-α-d-altropyranoside or its 3-²H derivative. A sequence involving a C-6 halogenation-dehydrohalogenation followed by catalytic hydrogenation of the resulting methyl 6-deoxy-α-d-arabino-hex-5-enopyranoside gave methyl 6-deoxy-β-l-galactopyranoside (methyl β-l-fucopyranoside) and then α-l-fucose, with an overall yield of 24% with respect to the starting methyl α-d-mannopyranoside.     

Efficient synthesis of a 6-deoxytalose tetrasaccharide related to the antigenic O-polysaccharide produced by Aggregatibacter actinomycetemcomitans serotype c

Concise synthesis of a 6-deoxy-α-l-talose tetrasaccharide, 6-deoxy-α-l-Talp-(1→3)-6-deoxy-α-l-Talp-(1→2)-6-deoxy-α-l-Talp-(1→3)-6-deoxy-α-l-Talp, the dimer of the disaccharide repeating unit of the OPS from Aggregatibacter actinomycetemcomitans serotype c, has been accomplished through suitable protecting group manipulations and stereoselective glycosylation starting from commercially available l-rhamnose. The target oligosaccharide in the form of its p-methoxyphenyl glycoside is suitable for further glycoconjugate formation via selective cleavage of this group.     

Synthesis of higher-carbon sugars via vinyltin derivatives of simple monosaccharides

6-O-Benzyl-7,8-dideoxy-1,2:3,4-di-O-isopropylidene-l-glycero-α-d-galacto-oct-7-ynopyranose reacted with tributyltin hydride to afford (Z-6-O-benzyl-7,8-dideoxy-1,2:3,4-di-O-isopropylidene-8-(tributylstannyl)-l-glycero-α-d-galacto-oct-7-enopyranose, which was subsequently isomerized to the E-olefin 4. Replacement of the tributyltin moietey with lithium in 4 afforded the vinyl anion which reacted with 3-O-benzyl-1,2-O-isopropylidene-α-d-xylo-pentodialdo-1,4-furanose, furnishing 3-O-benzyl-6-C-[(E)-6-O-benzyl-7-deoxy-1,2:3,4-di-O-isopropylidene-l-glycero-α-d-galacto-heptopyranos-7-ylidene] -60-deoxy-1,2-O-isopropylidene-α-d-gluco- (6) and -β-l-ido-furanose (7) in yields of ∼70 or ∼87% (depending on the temperature of the reaction). The configurations of the new chiral centers in 6 and 7 were determined by their conversion into 3-O-benzyl-1,2-O-isopropylidene-α-d-gluco- and -β-l-ido-furanose, respectively. Oxidation of 6 and 7 gave the same enone, 3-O-benzyl-6-C-[(E)-6-O-benzyl-7-deoxy-1,2:3,4-di-O-isopropylidene-l-glycero-α-d-galacto- heoptopyranos-7-ylidene]-6-deoxy-1,2-O-isopropylidene-α-d-xylo-hexofuranos-5-ulose.     

Groove-type Recognition of Chlamydiaceae-specific Lipopolysaccharide Antigen by a Family of Antibodies Possessing an Unusual Variable Heavy Chain N-Linked Glycan

The structure of the antigen binding fragment of mAb S25-26, determined to 1.95 Å resolution in complex with the Chlamydiaceae family-specific trisaccharide antigen Kdo(2→8)Kdo(2→4)Kdo (Kdo = 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid), displays a germ-line-coded paratope that differs significantly from previously characterized Chlamydiaceae-specific mAbs despite being raised against the identical immunogen. Unlike the terminal Kdo recognition pocket that promotes cross-reactivity in S25-2-type antibodies, S25-26 and the closely related S25-23 utilize a groove composed of germ-line residues to recognize the entire trisaccharide antigen and so confer strict specificity. Interest in S25-23 was sparked by its rare high μm affinity and strict specificity for the family-specific trisaccharide antigen; however, only the related antibody S25-26 proved amenable to crystallization. The structures of three unliganded forms of S25-26 have a labile complementary-determining region H3 adjacent to significant glycosylation of the variable heavy chain on asparagine 85 in Framework Region 3. Analysis of the glycan reveals a heterogeneous mixture with a common root structure that contains an unusually high number of terminal αGal-Gal moieties. One of the few reported structures of glycosylated mAbs containing these epitopes is the therapeutic antibody Cetuximab; however, unlike Cetuximab, one of the unliganded structures in S25-26 shows significant order in the glycan with appropriate electron density for nine residues. The elucidation of the three-dimensional structure of an αGal-containing N-linked glycan on a mAb variable heavy chain has potential clinical interest, as it has been implicated in allergic response in patients receiving therapeutic antibodies.     

Synthesis of trisaccharides containing 3-deoxy- -manno-2-octulosonic acid residues related to the KDO-region of enterobacterial lipopolysaccharides

Glycosylation of methyl (allyl 7,8-O-carbonyl-3-deoxy-α- -manno-2-octulopyranosid)onate with an α-(2→4) linked per-O-acetylated KDO-disaccharide bromide derivative under Helferich conditions afforded a 2:1 mixture of the α- and β-linked trisaccharide derivatives in 50% yield. Removal of the protecting groups gave sodium O-[sodium (3-deoxy-α- -manno-2-octulopyranosyl)onate]-(2→4)-O-[sodium (3-deoxy-α- and -β- -manno-2-octulopyranosyl)onate]-(2→4)-sodium (allyl 3-deoxy-α- -manno-2-octulopyranosid)onate. Radical copolymerization of the allyl glycosides afforded artificial antigens, suitable for defining antibody specificities directed against the KDO-region of enterobacterial lipopolysaccharides.     

Oligosaccharides from “standardized intermediates”. The 2-amino-2-deoxy- d-galactose analog of the blood-group O(H) determinant,type 2, and its precursors

The selectively benzylated glycoside allyl 2-acetamido-4,6-di-O-benzyl-2-deoxy-β- d-galactopyranoside ( 4) was prepared from the corresponding derivative of 2-acetamido-2-deoxy- d-glucose via the p-bromobenzenesulfonate and the benzoate. 2-O-Benzoyl-3,4,6-tri-O-benzyl-α- d-galactopyranosyl chloride ( 10) was obtained from allyl 6-O-benzyl-2-O-(2-butenyl)-α- d-galactopyranoside via known intermediates. To complete the sequence, the 1-propenyl 3,4,6-tri-O-benzyl galactoside was successively converted into the 2-benzoate, the free sugar, and the chloride 10. A fully protected form ( 11) of the trisaccharide α- l-Fucp-(1→2)-β- d-Galp-(1→4)- d-GalNAc was then synthesized by coupling 10 to 4, partially deblocking the disaccharide product, and l-fucosylating the resulting intermediate. Cleavage of the O-benzyl groups from 11, with concomitant saturation of the allyl group, gave the propyl β-glycoside of the unsubstituted trisaccharide.     

Changes in the hemicellulosic polysaccharides of rye-grass with increasing maturity

Reaction of the C-2 mercurated methyl hexopyranoside acetates 1–3 with an excess of iodine resulted in nearly quantitative replacement of mercury by iodine with retention and inversion of configuration at C-2. Similar replacement was observed with 2-acetoxymercuri-3,4,6-tri-O-acetyl-2-deoxy-α-d-glucopyranose (4). In the iodinolysis of 2-acetoxymercuri-1,3,4,6-tetra-O-acetyl-2-deoxy-α-d-glucopyranose (5) in methanol, however, replacement at C-2 was accompanied to a considerable extent by solvolysis of the 1-acetoxyl group, and a mixture of 1,2-trans isomers of methyl 3,4,6-tri-O-acetyl-2-deoxy-2-iodo-hexopyranosides having the d-gluco and d-manno configurations was obtained, together with 1,3,4,6-tetra-O-acetyl-2-deoxy-2-iodo-α-d-mannopyranose.     

The genus-specific lipopolysaccharide epitope of Chlamydia is assembled in C. psittaci and C. trachomatis by glycosyltransferases of low homology

Chlamydiae possess a genus-specific epitope that is located on the lipopolysaccharide (LPS) and is composed of a 3-deoxy-d -manno-octulosonic acid (Kdo) trisaccharide of the sequence αKdo-(2→8)–αKdo–(2→4)-αKdo. In Chlamydia trachomatis, this trisaccharide is biosynthetically generated through the action of a multi-functional Kdo-transferase encoded by the gene gseA. gseA of Chlamydia psittaci 6BC was cloned and expressed in a rough mutant (Re chemotype) of Escherichia coli (strain F515) that contains an LPS with only two α2→4-linked Kdo residues. Recombinant strains were able to add the immunodominant Kdo residue in a α2→8-linkage to the parental LPS, as determined by SDS–PAGE and Western blot analysis using a monoclonal antibody against the genus-specific epitope. The DNA sequence of gseA was determined and aligned to that published recently for C. trachomatis serovar L2. Most surprisingly, the two deduced amino acid sequences shared only an overall homology of 67%. Thus, gseA exhibits species specificity at the DNA level, whereas its gene product results in the synthesis of a carbohydrate antigen with genus specificity.     

Kdo hydroxylase is an inner core assembly enzyme in the Ko-containing lipopolysaccharide biosynthesis

The lipopolysaccharide (LPS) isolated from certain important Gram-negative pathogens including a human pathogen Yersinia pestis and opportunistic pathogens Burkholderia mallei and Burkholderia pseudomallei contains d-glycero-d-talo-oct-2-ulosonic acid (Ko), an isosteric analog of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo). Kdo 3-hydroxylase (KdoO), a Fe²⁺/α-KG/O₂ dependent dioxygenase from Burkholderia ambifaria and Yersinia pestis is responsible for Ko formation with Kdo₂-lipid A as a substrate, but in which stage KdoO functions during the LPS biosynthesis has not been established. Here we purify KdoO from B. ambifaria (BaKdoO) to homogeneity for the first time and characterize its substrates. BaKdoO utilizes Kdo₂-lipid IV_A or Kdo₂-lipid A as a substrate, but not Kdo-lipid IV_Ain vivo as well as in vitro and Kdo-(Hep)kdo-lipid A in vitro. These data suggest that KdoO is an inner core assembly enzyme that functions after the Kdo-transferase KdtA but before the heptosyl-transferase WaaC enzyme during the Ko-containing LPS biosynthesis.