Lipooligosaccharides (LOS) from the bacterium Rhizobium radiobacter Rv3 are structurally related to antigenic mammalian oligomannoses on the HIV-1 envelope glycoprotein spike that are targets for broadly neutralizing antibodies. Here, we prepared a hybrid structure of viral and bacterial epitopes as part of a vaccine design strategy to elicit oligomannose-specific HIV-neutralizing antibodies using glycoconjugates based on the Rv3 LOS structure. Starting from a Kdo2GlcNAc2 tetrasaccharide precursor, a central orthogonally protected mannose trichloroacetimidate donor was coupled to OH-5 of the innermost Kdo residue. To assemble larger glycans, the N-acetylamino groups of the glucosamine units were converted to imides to prevent formation of unwanted imidate byproducts. Blockwise coupling of the pentasaccharide acceptor with an α-(1→2)-linked mannotriosyl trichloroacetimidate donor introduced the D1-arm fragment. Glycosylation of O-6 of the central branching mannose with an α-(1→2)-α-(1→6)-linked mannotriosyl trichloroacetimidate donor unit then furnished the undecasaccharide harboring a D3-arm extension. Global deprotection yielded the 3-aminopropyl ligand, which was activated as an isothiocyanate or adipic acid succinimidoyl ester and conjugated to CRM197. However, representative oligomannose-specific HIV-neutralizing antibodies bound the undecasaccharide conjugates poorly. Possible reasons for this outcome are discussed herein along with paths for improvement.
Lipooligosaccharides (LOS) from the bacterium Rhizobium radiobacter Rv3 are structurally related to antigenic mammalianoligomannoses on the HIV-1envelope glycoprotein spike that are targets for broadly neutralizing antibodies. Here, we prepared a hybrid structure of viral and bacterial epitopes as part of a vaccine design strategy to elicit oligomannose-specific HIV-neutralizing antibodies using glycoconjugates based on the Rv3 LOS structure. Starting from a Kdo2GlcNAc2 tetrasaccharide precursor, a central orthogonally protected mannose trichloroacetimidatedonor was coupled to OH-5 of the innermost Kdo residue. To assemble larger glycans, the N-acetylamino groups of the glucosamine units were converted to imides to prevent formation of unwanted imidate byproducts. Blockwise coupling of the pentasaccharide acceptor with an α-(1→2)-linked mannotriosyl trichloroacetimidatedonor introduced the D1-arm fragment. Glycosylation of O-6 of the central branching mannose with an α-(1→2)-α-(1→6)-linked mannotriosyl trichloroacetimidatedonor unit then furnished the undecasaccharide harboring a D3-arm extension. Global deprotection yielded the 3-aminopropyl ligand, which was activated as an isothiocyanate or adipic acid succinimidoyl ester and conjugated to CRM197. However, representative oligomannose-specific HIV-neutralizing antibodies bound the undecasaccharide conjugates poorly. Possible reasons for this outcome are discussed herein along with paths for improvement.
HIV-1 remains a major
threat to human health in many countries,
and it is generally agreed that only a prophylactic vaccine is likely
to curb infection rates globally.[1,2] To be effective,
an HIV vaccine may need to elicit both humoral and cellular immune
responses to blunt infection and protect against disease. The sole
target for protective anti-HIV antibodies is the virus envelope spike
(Env),[3] a densely glycosylated trimer of
heterodimeric gp120 and gp41 subunits. The glycans on Env derive from
the biosynthetic machinery of the mammalian host cell and are meant
to allow the virus to evade the host antibody response.[4] As such, it was long thought that these glycans
are immunologically silent.[5] However, over
the last several years, it has become evident that some HIV-infected
individuals develop neutralizing antibodies to this “glycan
shield”.[6] 2G12 was the first human
monoclonal antibody described that targets the glycans on HIV Env.[7] Later studies showed that 2G12 binds an array
of oligomannoses on Env.[8] Following an
extended period without any description of 2G12-like antibodies, the
past decade has seen a sharp increase in the discovery of additional
neutralizing antibodies, some with substantial breadth and potency,
targeting what is now defined as the “high-mannose patch”
on HIV gp120.[9] Consequently, the high-mannose
patch has gained substantial attraction as a target for vaccine development.[10] The lipooligosaccharide (LOS) of the phytopathogenic Rhizobium radiobacter strain Rv3 was shown previously to
consist of a mannotetraose subunit α-Man-(1→2)-α-Man-(1→2)-α-Man-(1→3)-α-Man
that resembles the so-called D1 arm of mammalianoligomannose (Figure ).[11] The antigenic similarity to mammalianoligomannose was
shown by binding to 2G12, which is specific for the D1 arm oligomannose,
and later confirmed by the crystal structure of the bacterial mannotetraose
fragment in complex with 2G12.[12] The crystal
structure of the bacterial ligand was then used to model and construct
derivatives that would more closely resemble oligomannose, for example,
by including a D3-arm surrogate to position 6 of the central mannose
unit (Figure ).[13]
Figure 1
Structure of the LOS from R. radiobacter strain
Rv3 (left) and of full-sized N-linked mammalian oligomannose (Man9GlcNAc2) (right). Dashed lines indicate substoichiometric
substitution of the LOS by a mannosyl residue at O-6 of the central branching mannose and a galactosyl residue at O-8 of the side chain Kdo.
Structure of the LOS from R. radiobacter strain
Rv3 (left) and of full-sized N-linked mammalianoligomannose (Man9GlcNAc2) (right). Dashed lines indicate substoichiometric
substitution of the LOS by a mannosyl residue at O-6 of the central branching mannose and a galactosyl residue at O-8 of the side chain Kdo.A small library of two pentamannosides and four heptamannosides
was synthesized previously as spacer-equipped ligands, which were
then converted into their respective BSA conjugates.[13] BSA neoglycoconjugates containing the heptasaccharide α-Man-(1→2)-α-Man-(1→2)-α-Man-(1→3)-[α-Man-(1→2)-α-Man-(1→6)-α-Man-(1→6)]-β-Man
were bound best by the broadly neutralizing antibody PGT128 and related
antibodies that target the oligomannose patch on Env.[13] Lesser binding of the antibodies to a related heptasaccharide
conjugate containing the reducing mannose unit in the α-anomeric
configuration—as present in the bacterial glycan—suggested
that the β-anomeric configuration better mimics the cognate
epitope in this context. Nevertheless, it was possible to crystallize
the soluble α-anomeric heptamannoside ligand (dubbed NIT68A)
in complex with PGT128, which showed that the interactions between
antibody and the antigenic mimic versus mammalianoligomannose are
essentially superimposable.[13] Human-antibody
transgenic animals immunized with the β-anomeric heptamannoside
conjugate yielded antibodies with the capacity to neutralize a few
HIV strains, albeit at generally modest titers.[13]Based on encouraging results from the series of studies
summarized
above, we have now set out to construct neoglycoconjugates that incorporate
a distinctive bacterial constituent. Our goal is to obtain derivatives
that more closely resemble bacterial LOS, thus increasing the “foreignness”
of the glycosides and, presumably, their immunogenic potential. Our
strategy is based on mimicry of host glycans by bacterial glycans,
which trigger relatively robust antibody responses to otherwise poorly
immunogenic epitopes. For example, animals immunized with purified Campylobacter jejuni LOS produce sustained levels of anti-LPS
antibodies with ganglioside cross-reactivity.[14] Similarly, animals immunized with Helicobacter pylori cells or purified H. pylori LPS produce robust
antibodies with capacity to bind Lewis X or Y antigens on human cells
and tissue.[15]We recently communicated
the chemical synthesis of the rhizobialpentasaccharide LOS core comprising the central α-Man-(1→5)-linkedKdo2GlcNAc2 unit.[16] The protected pentasaccharide had already been equipped with an
orthogonal protecting group pattern at the central mannose which would
allow the further extension at position 3 with the D1 arm and thus
enable access to a defined material of the rhizobialoctasaccharide
LOS. Moreover, selective removal of a 6-O-silyl ether
had been foreseen which would open an access to incorporate the D3-arm
surrogate chain. Here, we describe the chemical synthesis of this
novel undecasaccharide, featuring a hybrid structure of viral and
bacterial epitopes, its conversion into a CRM197 neoglycoconjugate
and binding studies with the HIV-broadly neutralizing antibody PGT128
and other select members of the PGT128/PGT130 neutralizing antibody
family.
Results and Discussion
Aiming first at the rhizobialoctasaccharide target, the previously
reported pentasaccharide 1, containing the α-(1→5)-linked,
orthogonally protected mannose unit, was subjected to DDQ oxidation
to liberate position 3 for further extension (Scheme ). Removal of the 3-O-(2-methylnaphthyl)
group, however, could not be executed to full conversion, as degradation
reactions started to occur leading to partial and complete loss of
the isopropylidene groups at the lateral Kdo residue. By application
of a mild basic buffer (PBS, pH = 7.2), hydrolysis was largely suppressed
and compound 2 was eventually isolated in 65% yield by
column chromatography with recovery of unreacted starting material
(22%). The pronounced lability of the acetonide groups was also observed
for solutions of 1 in CDCl3 in an NMR tube
upon standing for several hours. Hence, glycosyl acceptor 2 was directly used for the ensuing coupling reaction with the previously
described[13] mannotriosyl trichloroacetimidatedonor 3 in a [5 + 3] block assembly. Promotion of the
glycosylation reaction either with TMSO triflate (0.15–2 equiv)
or BF3·Et2O (2 equiv), respectively, resulted
in formation of several byproducts and poor yields of glycoside. As
the main reaction product, imidate-connected pseudo-octasaccharide 4 could be isolated in 37% yield from the reaction mixture
together with unreacted acceptor 2 (23%). The structure
of the imidate 4 was derived from proton and carbonNMR
data, which revealed the loss of one NH signal of the GlcNAc-backbone
and showed a significant low-field shift of the anomeric proton of
mannose B (6.49 ppm). This anomeric signal showed an HMBC correlation
to a quaternary carbon signal at 162.2 ppm that was additionally correlated
to a 1HNMR signal of a methyl group at 2.15 ppm. Furthermore,
in an HSQC experiment, the methyl protons were found to be connected
to an upfield-shifted carbon signal at 15.6 ppm. These data mirror
previously reported NMR characteristics of 2-N-glycosyl
imidates and rule out the formation of an N-glycosidic
linkage.[17] The attachment site at the distal
glucosamine unit could be unambiguously identified, as tracking of
the spin system of the reducing GlcNAc unit could be followed from
the anomeric proton to the NH signal at C-2 via COSY correlations.
The imidate formation also had a significant impact on the chemical
shift of C-2 of the distal glucosamine unit, which was observed at
63.8 ppm, thus in a range not usually observed for N-linked carbons. In contrast, the 13CNMR signal of C-2
of the reducing GlcNAc moiety was observed at 51.8 ppm. Thus, the
α-linked 3-azidopropyl spacer group most likely had sterically
blocked the imidate formation at the reducing residue, and only a
single imidate had been formed. This notorious side reaction of N-acetyl amino groups has been observed previously and is
deemed responsible for the low reactivity of N-acetylatedglycosyl acceptor derivatives in glycosylation reactions.[18,19]
Scheme 1
Imidate Formation and Synthesis of Pentasaccharide Acceptor 6
To prevent imidate
formation, conversion of N-acetamido
groups into imides has been suggested; these can be readily reconverted
into the N-acetamido derivatives under mild alkaline
conditions.[20] Reaction of pentasaccharide 1 with acetyl chloride in the presence of Hünig base
proceeded smoothly and afforded the bis-N-acetylated
derivative 5 in 89% yield. Similar to the imidate product 4, the 13CNMR signal of C-2 of the distal GlcNAc
unit B was observed downfield shifted (61.9 ppm), whereas the signal
of the reducing GlcNAc residue was detected at 56.9 ppm. The pronounced
anisotropic effect of the second acetamido group on the β-anomeric
glycoside was also reflected in a significant downfield shift of its
anomeric proton, which was observed at 5.32 ppm with a coupling constant
of 7.7 Hz in agreement with a trans-diaxial spin
coupling interaction. Next, the 3-O-Nap group of
the α-mannose residue was oxidatively cleaved in a buffered
system and produced the glycosyl acceptor 6 in 73% yield.Glycosylation of 6 using 2 equiv of the mannotriosyldonor 3 and TMSO triflate as promoter was performed in
dichloromethane in the presence of molecular sieves 4 Å at room
temperature and afforded the α-(1→3)-connected octasaccharide
derivative 7 in a good yield of 69% (Scheme ). The α-anomeric configuration
of the (1→3)-linkedmannose unit of 7 was confirmed
by the value of the heteronuclear JC-1,H-1 coupling constant (173.3 Hz) measured in an HMBC experiment.[21] Deprotection of 7 was achieved
by treatment with 90% aqueous TFA, which removed the 6-O-tert-butylsilyl ether as well as both isopropylidene
groups of the side-chain Kdo residue and furnished pentaol 8 in 85% yield. Full deprotection was eventually accomplished by sequential
Zemplén transesterification with sodium methoxide to remove
benzoyl, carbonate, and acetyl groups, hydrogenation under flow conditions,
and alkaline hydrolysis of the Kdo methyl ester groups to afford the
target octasaccharide 9 in 60% yield after final purification
by size-exclusion chromatography on LH-20. 1H and 13CNMR data of the octasaccharide were assigned fully using
COSY, TOCSY, HSQC, and HMBC experiments (see Table S1, Supporting Information) and were in generally good agreement
with the published data of the R. radiobacter Rv3
oligosaccharide.[11] As expected, differences
were noted for the glucosamine–phosphate backbone (see Figure ) and carbon 8 of
the lateral Kdo, which is partially substituted by an additional β-galactopyranosyl
residue in the rhizobial LOS. The reported assignment of C-6 for the
distal glucosamine unit at 70.5 ppm, however, was empirically based
and needs to be corrected as the ketosidic linkage of Kdo induces
only a very minor glycosylation shift of the connected carbon (63.01
ppm).[22] This assignment was corroborated
by an HMBC correlation of a separate H-6b signal of the distal GlcNAc
unit at 3.49 ppm to the anomeric signal of Kdo A. Carbons 4 and 5
of the dibranched internal Kdo unit A were shifted downfield to 71.26
and 74.40 ppm, respectively, in good agreement with literature data
of comparable 4,5-O-disubstituted Kdo fragments.[23]
Scheme 2
Synthesis of Rhizobial LOS Octasaccharide
Fragment 9
Initially, we had envisaged to next introduce the D3 chain
after
selective cleavage of the 6-O-TBS group in 7, which should readily give access to glycosyl acceptor 10. Despite many attempts using various reagents and reaction
conditions, a selective desilylation could not be accomplished in
a reasonable yield, due to the lability of the isopropylidene protecting
groups under acidic conditions and also partial removal of the N-acetamido groups under basic conditions (see Table S2). As a contingency measure, introduction
of the bis-acetonide using pentaol 8 was also attempted
but did not lead to formation of compound 10. Because
of this impasse, we abandoned the original approach and redesigned
the assembly of the pentasaccharide precursor without the isopropylidene
protection of the lateral Kdo unit.Although the well-established
per-O-acetylatedKdo bromide methyl ester 11 exerts low α-selectivity
and is prone to facile elimination, leading to the corresponding 2,3-dehydro
derivative, the glycosylation under Helferich conditions is nevertheless
a robust approach.[24] Reaction of 6 equiv
of donor 11 with the previously synthesized trisaccharide
acceptor derivative 12(16) in
dry acetonitrile in the presence of a 4.5:1 mixture of Hg(CN)2/HgBr2 in dichloromethane at room temperature gave
regioselectively 68% of the α-linked tetrasaccharide 13 together with 11% of the corresponding β-anomer (Scheme ). The anomeric mixture
was resolved by column chromatography, and the anomeric configuration
was assigned on the basis of the downfield shifted 1HNMR
signal of H-4 (5.25 ppm for 13 and 4.85 ppm for the β-anomer)
as well as the 1HNMR chemical shifts of the equatorial
3-deoxy protons (2.25 ppm for 13 and 2.41 ppm for the
β-isomer).[25,26]
Scheme 3
Synthesis of Alternative
Pentasaccharide Acceptor 17
Glycosylation of the axial Kdo 5-OH group of 13 could
next be accomplished with the previously reported mannosyl trichloroacetimidatedonor 14 equipped with a 1,2-trans-directing
2-O-benzoyl group.[13] The
glycosylation reaction—promoted by TMSO triflate in dichloromethane
in the presence of molecular sieves 4 Å—proceeded to give
pentasaccharide 15 in 56% yield and also allowed recovery
of unreacted 13 (16%). Next, both N-acetamido
groups were converted into the bis-imide derivative by treatment of 15 with acetyl chloride and Hünig base in dichloromethane
to afford fully blocked pentasaccharide 16 in 89% yield.
Oxidative removal of the 3-O-Nap group from 16 with DDQ furnished the stable pentasaccharide acceptor 17 in an improved yield (79%) compared to the similar transformation
performed with 2.For the envisaged introduction
of the D3 arm surrogate, the α-(1→2)-α-(1→6)-linkedmannotriosyl trichloroacetimidate 21 donor[27] was prepared. The donor was formed by a first
coupling step of the known α-(1→2)-connected trichloroacetimidate 18(28) with the orthogonally protected
primary alcohol 19. Thioglycoside 19 was
prepared according to the literature[16,29] and was equipped
with a 3-O-naphthylmethyl protecting group, which
could eventually also serve for incorporation of the D2 arm. Glycosylation
of 19 was promoted by catalytic TMSOTf at room temperature
in dichloromethane and afforded the α-(1→6)-linkedmannotrioside 20 in 72% yield (Scheme ).
Scheme 4
Synthesis of Trisaccharide Donor 21
The α-anomeric configuration
of the internal mannoside was
again safely assigned on the basis of the JC-1,H-1 coupling constant (172 Hz). A coupling reaction of 1.8 equiv of
thioglycoside 20 to pentasaccharide 17 promoted
by NIS/TfOH afforded a low yield (28%) of the octasaccharide product,
which suggested to switch to the trichloroacetimidatedonor. Hence,
the anomeric thiotolyl group was cleaved by treatment with N-iodosuccinimide/TFA followed by conversion into the corresponding
TCAdonor 21 by subsequent reaction with trichloroacetonitrile/K2CO3 in a combined yield of 59% for two steps. Proceeding
toward the undecasaccharide target, pentasaccharide 17 was first coupled with the acyl-protected α-(1→2)-α-(1→2)-linkedmannotriosyl trichloroacetimidate 3 in the presence
of catalytic TMSOTf and molecular sieves 4 Å in dichloromethane,
which produced the fully protected octasaccharide along with the 6-O-desilylated derivative 22 (Scheme ). The mixture was directly
subjected to the desilylation step by acidic hydrolysis with 90% aqueous
TFA, and octasaccharide 22 was isolated in a combined
yield of 51%. The 600 MHz 1HNMR spectrum in CDCl3 revealed significantly broadened signals for several mannose residues
which prevented a reliable purity assessment. Spectra with improved
resolution, however, could be recorded for solutions in toluene-d8. Thus, the 3-O-glycosylation
site at the central mannose A could be confirmed by the downfield
shift of H-2 at 6.02 ppm, which was in the same range as for the remaining O-benzoylated positions as well as the downfield-shifted 13C signal of carbon 3 at 76.7 ppm. This way, a potential 2→3 O-benzoyl migration could be ruled out. The final blockwise
[8 + 3] glycosylation was successfully performed under similar glycosylation
conditions using the octasaccharide acceptor 22 and the
trisaccharidetrichloroacetimidatedonor 21.
Scheme 5
Synthesis
of Undecasaccharide 24
Thus, the fully protected undecasaccharide 23 was
obtained in a yield of 77%, and its proton spectra were of sufficient
resolution to allow for a detailed assignment. The attachment site
of the branching mannose could be confirmed by the observed glycosylation
shift of C-6 (67.1 ppm) which was similar as for the adjacent mannose
unit E (for labeling of the mannosyl residues, see the Experimental Section) at 66.2 ppm.Global
deprotection was performed consecutively with intermediate
control of reaction progress by NMR spectroscopy. First, acetimido,
acetyl, carbonate, and benzoyl groups were removed by transesterification
under Zemplén conditions that required 3 days at room temperature
until completion. Next, benzyl and the NAP ether were removed by hydrogenolysis
on 10% Pd carbon in a mixture of aqueous methanol/acetic acid under
flow-conditions, until aromatic signals could not further be detected
by NMR. Finally, saponification of the methyl ester groups in aqueous
NaOH led to the fully deprotected undecasaccharide 24 isolated in 43% yield for the last three steps after HILIC purification.
A full assignment of the deprotected undecasaccharide 24 suffered from severe overlap of signals, but key assignments could
still be achieved, and furthermore, superposition of HSQC spectra
with octasaccharide 9, the previously synthesized core
pentasaccharide[16] ManKdo2GlcNAc2 and the 3-aminopropyl mannoheptaoside fragment[13] allowed for cross-checking the NMR assignments.
Specifically, an HMBC correlation of the anomeric proton at 4.89 of
mannose unit E to a downfield shifted methylene carbon of mannose
A at 65.9 ppm was observed, confirming position 6 as the linkage site
of the D3 arm. Anomeric proton and carbon signals of mannose units
B-G of 24 where nearly unchanged when compared to the manno-heptasaccharide, but the different environment of
the central mannose A linked to Kdo had a pronounced effect. Whereas 1H/13C signals of the heptasaccharide ligand were
observed at 4.78/100.7 ppm, signals of mannose A were downfield shifted
to 5.14/101.7 ppm, probably due to the close proximity of the neighboring
carboxylate of Kdo.To assess the antigenic properties of the
undecasaccharide ligand,
the corresponding neoglycoconjugates were prepared using two different
activation protocols for the conjugation step. Reaction conditions
were chosen to incorporate a limited amount of antigen so as not to
introduce glycosidic clusters that may yield unwanted neo-glycoepitopes
in prospective immunization studies. Thus, spacer glycoside 24 was reacted with thiophosgene/NaHCO3 to give
an intermediate isothiocyanate derivative which was then incubated
with nontoxic mutant of diphtheria toxin CRM197 as protein
carrier[30,31] to give neoglycoconjugate 25. Due to the size of the ligand, separation of unreacted ligand from
the neoglycoconjugate had to be achieved by spin-filtration. Alternatively, 24 was first reacted with adipic acid bis(N-hydroxysuccinimide) ester 26 to afford the activated
half-ester intermediate followed by coupling to the protein. MALDI-TOF
analysis of the conjugates (Figure S1)
revealed a comparable ligand copy number of ∼3.8 for 25 and ∼4.1 for 27, respectively (Scheme ).
Scheme 6
Synthesis of Neoglycoconjugates 25 and 27 and Structure of Neoglyconjugate 28
As done previously,[13] we screened the
two neoglycoconjugates by ELISA for recognition by broadly neutralizing
antibodies PGT125, -126, -128, and -130, which target the high-mannose
patch on HIV but interact with the oligomannose in slightly different
ways.[32,33] A CRM197 conjugate of the oligomannosidic
heptasaccharide 28 was used as a comparator, as separate
investigations had shown that the four aforementioned antibodies bind
this conjugate, dubbed NIT211, as avidly as the earlier BSA conjugate
of the same glycoside (unpublished findings). Whereas the four antibodies
bound NIT211 avidly as expected, antibody binding to the undecasaccharide
conjugates was unexpectedly poor (Figure ); only PGT130 exhibited measurable binding
in this assay setup.
Figure 2
Broadly neutralizing antibodies PGT125, -126, -128, and
-130 bind
with relatively low avidity to CRM197 conjugates of the
undecasaccharide composed of an oligomannosidic heptasaccharide with
a Kdo2GlcNAc2 backbone. All four antibodies
were tested as IgGs. NIT269 and NIT273 represent the isothiocyanate-conjugated
and the adipate-conjugated glycoside, respectively. NIT211, used as
a comparator, is the heptamannoside conjugated via isothiocyanate
to CRM197.
Broadly neutralizing antibodies PGT125, -126, -128, and
-130 bind
with relatively low avidity to CRM197 conjugates of the
undecasaccharide composed of an oligomannosidic heptasaccharide with
a Kdo2GlcNAc2 backbone. All four antibodies
were tested as IgGs. NIT269 and NIT273 represent the isothiocyanate-conjugated
and the adipate-conjugated glycoside, respectively. NIT211, used as
a comparator, is the heptamannoside conjugated via isothiocyanate
to CRM197.To exclude influences imparted by conjugation to carrier,
we performed
ELISA inhibition assays with undecasaccharide 24 in comparison
to the soluble oligomannosidic heptasaccharide conjugate 28. As expected, and consistent with previous findings,[13] binding of all four antibodies to microtiter
plates coated with conjugate NIT211 was readily inhibited (Figure S2). In contrast, no inhibition was observed
with the undecasaccharide, thus corroborating the poor antibody binding
observed with the corresponding CRM197 conjugate.We sought to arrive at a reasonable model for understanding these
results based on structural considerations. To do so, a model of the
putative interaction of PGT128 with the undecasaccharide was constructed
based on the crystal structure complex of the antibody with a heptamannoside
ligand (PDB ID 6B3D) and using separate crystallized fragments of the Kdo disaccharide
and the lipid A backbone to guide our modeling of these portions of
the undecasaccharide (Figure ).
Figure 3
Interaction of HIV-broadly neutralizing antibody PGT128 with a
model of the undecasaccharide. (a) Overview of the modeled interaction.
The crystal structure complex of PGT128 with heptamannoside NIT68A[13,34] was used as template to create the model. The heavy and light chains
of the PGT128 Fab are shown in a ribbon representation in dark gray
and light gray, respectively. The modeled undecasaccharide is shown
in stick representation, with the NIT68A heptamannoside in yellow,
Kdo disaccharide in green, and the GlcN disaccharide in blueish purple.
(b) Close-up view showing the modeled interaction of PGT128 with the
undecasaccharide. The constituents of the undecasaccharide are labeled.
To model the Kdo disaccharide, a crystallized Hep-Kdo2 fragment[35] was modeled into the PGT128 binding site by
superposing the heptose residue (pink) onto the central branching
mannose of the NIT68A structure. To model the lipid A disaccharide,
a crystallized Kdo-GlcN2 fragment[36] was superposed onto the structure using the main-chain Kdo residue
(Kdo I; orange) as a guide. (c) Left side view of panel b, highlighting
the assumed proximity of the side chain Kdo (Kdo II) to the antibody.
Interaction of HIV-broadly neutralizing antibody PGT128 with a
model of the undecasaccharide. (a) Overview of the modeled interaction.
The crystal structure complex of PGT128 with heptamannosideNIT68A[13,34] was used as template to create the model. The heavy and light chains
of the PGT128Fab are shown in a ribbon representation in dark gray
and light gray, respectively. The modeled undecasaccharide is shown
in stick representation, with the NIT68Aheptamannoside in yellow,
Kdo disaccharide in green, and the GlcN disaccharide in blueish purple.
(b) Close-up view showing the modeled interaction of PGT128 with the
undecasaccharide. The constituents of the undecasaccharide are labeled.
To model the Kdo disaccharide, a crystallized Hep-Kdo2 fragment[35] was modeled into the PGT128 binding site by
superposing the heptose residue (pink) onto the central branching
mannose of the NIT68A structure. To model the lipid A disaccharide,
a crystallized Kdo-GlcN2 fragment[36] was superposed onto the structure using the main-chain Kdo residue
(Kdo I; orange) as a guide. (c) Left side view of panel b, highlighting
the assumed proximity of the side chain Kdo (Kdo II) to the antibody.The modeling suggests that the
side-chain Kdo (Kdo II) clashes
with the antibody, in particular with HCDR2, and that, because of
spatial constraints, it also may bump into the central branching mannose
residue, thus likely altering the antigenic presentation of the rest
of the molecule. Consistent herewith is the NMR data, showing that,
with one exception, all mannose shifts for undecasaccharide are superimposable
with those of the previous heptasaccharide. The noted exception is
the central branching mannose (ManA), supporting the notion that the
side chain Kdo is interfering with proper PGT128 binding. PGT130,
which bound undecasaccharide conjugates somewhat better than PGT128
(or the other two antibodies), is believed to recognize high-mannoseglycans in a mode somewhat similar to PGT128.[33] However, PGT130 notably lacks a 6-amino-acid insertion in HCDR2
that typifies PGT128 (and the other two antibodies), which may make
it better able to accommodate the side chain Kdo and thus bind the
undecasaccharide conjugates somewhat better than the other antibodies.
Conclusions
In this study, we have undertaken a blockwise assembly of an undecasaccharide
harboring a common structurally conserved fragment of bacterial lipopolysaccharides
extended by two oligomannose chains. Whereas the blockwise glycosylation
steps using oligomannosyl trichloroacetimidatedonors proceeded in
good yields and high stereoselectivity, the synthetic route had to
be modified in order to prevent imidate formation at one of the N-acetylglucosamine units in the glycosyl acceptor molecules.
Conversion into the corresponding bis-N-acetylated
derivatives allowed for the ensuing glycosylation steps and protecting
group manipulation. In addition, isopropylidene-protecting groups
at the lateral Kdo unit were not sufficiently stable to allow further
chain elongation reactions and had to be replaced by acetyl groups.
Deprotection allowed the synthesis and full NMR characterization of
the octasaccharide fragment related to rhizobiallipooligosaccharide
as well as the targeted undecasaccharide that was eventually converted
into CRM197 neoglycoconjugates for immunochemical studies.
We used the oligomannose-specific HIV-neutralizing antibodies PGT125,
-126, -128, and -130 as sentinels to gauge proper antigenic presentation
of the oligomannose mimic. We observed no antibody binding (PGT125,
-126, and -128) or only low antibody binding (PGT130). Modeling suggests
that removing the side chain Kdo could restore antigenicity, and thus,
the synthesis of such variants is now underway.
Authors: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376
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