Syntheses and evaluation of biantennary oligosaccharide ligands mimicking sialyl Lewis X.

Sialyl Lewis X (1) is known to be a ligand of the cell adhesion molecule E-selectin. We have synthesized several biantennary glycoside-terminated ligands mimicking sialyl Lewis X (1), and evaluated their binding activity to E-selectin using HL-60 cells expressing sialyl Lewis X epitope and human umbilical vein endothelial cells (HUVECs). These compounds were found to possess moderate binding activities to E-selectin. Among them, di-fucoside analog (8) which has no sialic acid carboxylate group was more active than 2, which had both the sialyl-galactose residue and the fucose residue (IC50, 8: 4.7 mM, 2: 11.7 mM). Furthermore, in the rat pleuritic model in vivo induced by carrageenin, 8 was found to reduce neutrophil infiltration at inflammatory lesions.     

Synthesis of a Sialyl Lewis x Mimic with Fixed Carboxylic Acid Group: Chemical Approach toward the Elucidation of the Bioactive Conformation of Sialyl Lewis x

The relation of the solution and bioactive conformation of sialyl Lewis x (sLe(x)) has been addressed by chemical means. To mimic the preferred solution conformation of sLe(x) 1, the more rigid analog 2 has been designed and synthesized. The sialic acid residue of 1 was replaced by a carboxylic acid function which is fixed in the equatorial position of a six membered ring acetal fused to galactose. Due to entropic considerations, an increased biological activity could be expected if the preferred solution conformation and bound form of sLe(x) were similar. Since mimic 2 was found to be inactive in an E-selectin binding assay, the bound form of sLe(x) most probably differs from the prevailing solution conformation.     

Insights into molecular recognition of Lewis(X) mimics by DC-SIGN using NMR and molecular modelling

In this work, we have studied in detail the binding of two α-fucosylamide-based mimics of Lewis(X) to DC-SIGN ECD (ECD = extracellular domain) using STD NMR and docking. We have concluded that the binding mode occurs mainly through the fucose moiety, in the same way as Lewis(X). Similarly to other mimics containing mannose or fucose previously studied, we have shown that both compounds bind to DC-SIGN ECD in a multimodal fashion. In this case, the main contact is the interaction of two hydroxyl groups one equatorial and the other one axial (O3 and O4) of the fucose with the Ca(2+) as Lewis(X) and similarly to mannose-containing mimics (in this case the interacting groups are both in the equatorial position). Finally, we have measured the K(D) of one mimic that was 0.4 mM. Competitive STD NMR experiments indicate that the aromatic moiety provides additional binding contacts that increase the affinity.     

Synthesis of 1,1-linked galactosyl mannosides carrying a thiazine ring as mimetics of sialyl Lewis X antigen: investigation of the effect of carboxyl group orientation on P-selectin inhibition

This paper describes the synthesis of 1,1-linked galactosyl mannosides as sialyl Lewis X mimetics that contain a spiro-ring to position the carboxylate group in a well-defined orientation. It was found that compound 4 is more active as a P-selectin inhibitor (IC50 = 19 microM) than the parent disaccharide 2, which contains a flexible carboxyl group (IC50 = 193 microM). This result is consistent with that observed in the previous NMR study of sialyl Lewis X bound to P-selectin. The chemistry described here should be useful for the development of selective inhibitors of E-, P-, and L-selectins.     

NMR structure elucidation of cyclic sialyl 6-sulfo Lewis x, a biologically dormant form of L-selectin ligand

The structure of cyclic sialyl 6-sulfo Lewis x, a new biologically dormant form of L-selectin ligand, was determined unambiguously by the accurate NMR analysis to have the lactamized ^{[5.], (a), (b), [2.], (a) and (b)}B conformation of its sialic acid. For the NMR structure elucidation were used various informations, such as chemical shifts values, appearance of amide proton, and NOE.     

Conformation of glycomimetics in the free and protein-bound state: structural and binding features of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man

The conformational properties of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man in solution have been carefully analyzed by a combination of NMR spectroscopy and time-averaged restrained molecular dynamics. It has been found that both the alpha-1,3- and the alpha-1,6-glycosidic linkages show a major conformational averaging. Unusual Phi ca. 60 degrees orientations for both Phi torsion angles are found. Moreover, a major conformational distinction between the natural compound and the glycomimetic affects to the behavior of the omega(16) torsion angle around the alpha-1 --> 6-linkage. Despite this increased flexibility, the C-glycosyl analogue is recognized by three mannose binding lectins, as shown by NMR (line broadening, TR-NOE, and STD) and surface plasmon resonance (SPR) methods. Moreover, a process of conformational selection takes place, so that these lectins probably bind the glycomimetic similarly to the way they recognize the natural analogue. Depending upon the architecture and extension of the binding site of the lectin, loss or gain of binding affinity with respect to the natural analogue is found.     

Synthetic glycoprotein mimics inhibit L-selectin-mediated rolling and promote L-selectin shedding

L-selectin is a leukocyte cell-surface protein that facilitates the rolling of leukocytes along the endothelium, a process that leads to leukocyte migration to a site of infection. Preventing L-selectin-mediated rolling minimizes leukocyte adhesion and extravasation; therefore, compounds that inhibit rolling may act as anti-inflammatory agents. To investigate the potential role of multivalent ligands as rolling inhibitors, compounds termed neoglycopolymers were synthesized that possess key structural features of physiological L-selectin ligands. Sulfated neoglycopolymers substituted with sialyl Lewis x derivatives (3',6-disulfo Lewis x or 6-sulfo sialyl Lewis x) or a sulfatide analog (3,6-disulfo galactose) inhibited L-selectin-mediated rolling of lymphoid cells. Functional analysis of the inhibitory ligands indicates that they also induce proteolytic release of L-selectin. Thus, their inhibitory potency may arise from their ability to induce shedding. Our data indicate that screening for compounds that promote L-selectin release can identify ligands that inhibit rolling.     

Refinement of the conformation of UDP-galactose bound to galactosyltransferase using the STD NMR intensity-restrained CORCEMA optimization

The STD NMR technique has originally been described as a tool for screening large compound libraries to identify the lead compounds that are specific to target proteins of interest. The application of this technique in the qualitative epitope mapping of ligands weakly binding to proteins, virus capsid shells, and nucleic acids has also been described. Here we describe the application of the STD NMR intensity-restrained CORCEMA optimization (SICO) procedure for refining the bound conformation of UDP-galactose in galactosyltransferase complex using STD NMR intensities recorded at 500 MHz as the experimental constraints. A comparison of the SICO structure for the bound UDP-galactose in solution with that in the crystal structure for this complex shows some differences in ligand torsion angles and V253 side-chain orientation in the protein. This work describes the first application of an STD NMR intensity-restrained CORCEMA optimization procedure for refining the torsion angles of a bound ligand structure. This method is likely to be useful in structure-based drug design programs since most initial lead compounds generally exhibit weak affinity (millimolar to micromolar) to target proteins of pharmaceutical interest, and the bound conformation of these lead compounds in the protein binding pocket can be determined by the CORCEMA-ST refinement.     

Neoglycolipid probes prepared via oxime ligation for microarray analysis of oligosaccharide-protein interactions

Neoglycolipid technology is the basis of a microarray platform for assigning oligosaccharide ligands for carbohydrate-binding proteins. The strategy for generating the neoglycolipid probes by reductive amination results in ring opening of the core monosaccharides. This often limits applicability to short-chain saccharides, although the majority of recognition motifs are satisfactorily presented with neoglycolipids of longer oligosaccharides. Here, we describe neoglycolipids prepared by oxime ligation. We provide evidence from NMR studies that a significant proportion of the oxime-linked core monosaccharide is in the ring-closed form, and this form selectively interacts with a carbohydrate-binding protein. By microarray analyses we demonstrate the effective presentation with oxime-linked neoglycolipids of (1) Lewis(x) trisaccharide to antibodies to Lewis(x), (2) sialyllactose analogs to the sialic acid-binding receptors, siglecs, and (3) N-glycans to a plant lectin that requires an intact N-acetylglucosamine core.     

Targeting norovirus infection-multivalent entry inhibitor design based on NMR experiments

Noroviruses attach to their host cells through histo blood group antigens (HBGAs), and compounds that interfere with this interaction are likely to be of therapeutic or diagnostic interest. It is shown that NMR binding studies can simultaneously identify and differentiate the site for binding HBGA ligands and complementary ligands from a large compound library, thereby facilitating the design of potent heterobifunctional ligands. Saturation transfer difference (STD) NMR experiments, spin-lock filtered NMR experiments, and interligand NOE (ILOE) experiments in the presence of virus-like particles (VLPs), identified compounds that bind to the HBGA binding site of human norovirus. Based on these data two multivalent prototype entry-inhibitors against norovirus infection were synthesized. A surface plasmon resonance based inhibition assay showed avidity gains of 1000 and one million fold over a millimolar univalent ligand. This suggests that further rational design of multivalent inhibitors based on our strategy will identify potent entry-inhibitors against norovirus infections.     

Competition STD NMR for the detection of high-affinity ligands and NMR-based screening

The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing high-affinity ligand in the compound mixture can be detected by the disappearance or reduction of the STD signals of a low-affinity indicator ligand. This is demonstrated on a BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) protein-inhibitor system. This method can also be used to derive an approximate value, or a lower limit, for the dissociation constant of the potential ligand based on the reduction of the signal intensity of the STD indicator, which is illustrated on an HSA (human serum albumin) model system. This leads to important applications of the competition STD NMR method for lead discovery: it can be used (i) for compound library screening against a broad range of drug targets to identify both high- and low-affinity ligands and (ii) to rank order analogs rapidly and derive structure-activity relationships, which are used to optimize these NMR hits into viable drug leads.     

Blood group B galactosyltransferase: insights into substrate binding from NMR experiments

The biosynthesis of human blood group B antigens is accomplished by a highly specific galactosyltransferase (GTB). On the basis of NMR experiments, we propose a "molecular tweezers mechanism" that accounts for the exquisite stereoselectivity of donor substrate selection. Transferred NOE experiments for the first time reveal the bioactive conformation of the donor substrate UDP-galactose (UDP-Gal) and of its enzymatically inactive analogue, UDP-glucose (UDP-Glc). Both bind to GTB in a folded conformation that is sparsely populated in solution, whereas acceptor ligands bind in a conformation that predominates in solution. The bound conformations of UDP-Gal and UDP-Glc are identical within experimental error. Therefore, GTB must discriminate between the two activated sugars on the basis of a hitherto unknown transition state that can only be formed in the case of UDP-Gal. A full relaxation and exchange matrix analysis of STD NMR experiments reveals that acceptor substrates dissociate significantly faster (k(off) > 100 Hz) from the binding pocket than donor substrates (k(off) approximately 10 Hz). STD NMR experiments also directly show that proper recognition of the hexopyranose rings of the UDP sugars requires bivalent metal cations. At the same time, this analysis furnishes the complete three-dimensional structure of the enzyme with its bound donor substrate UDP-Gal on the basis of a prior crystal structure analysis. We propose that, upon acceptor binding, GTB uses the Asp 302 and Glu 303 side chains as "molecular tweezers" to promote bound UDP-Gal but not UDP-Glc into a transition state that leads to product formation.     

Glycopeptides as oligosaccharide mimics: high affinity sialopeptide ligands for sialoadhesin from combinatorial libraries

Two different sialic acid containing glycopeptide (sialopeptide) libraries were synthesized using the portion mixing method and ladder synthesis. The libraries were attached via an IMP spacer and a photolabile linker to PEGA(1900) resin in order to facilitate rapid and unambiguous structural analysis of hits by MALDI-TOFMS. One library contained a lactamized sialic acid moiety at the N terminus of a pentapeptide, while a second library displayed a sialic acid residue at the center of a heptapeptide. The sialopeptide libraries were screened against the recombinant binding domain (SnD1) of a sialic acid binding Ig-like protein, sialoadhesin (Siglec-1). No ligands were identified from the lactamized sialic acid library, underscoring the importance of the carboxylic acid moiety for binding. Screening of the second gave few distinct hits (approximately 0.03% of library) with a high consensus. The high-affinity ligands contained, in most cases, a WG motif following the sialylated Thr. The strength of binding of selected ligands was determined by surface plasmon resonance. The best sialopeptide ligand, WLLT(Sa)WGT, exhibited micromolar affinity of SnD1; >10 times the affinity of SnD1 to 3'-sialyl lactose.     

Synthesis and biological evaluation of a new sialyl Lewis X mimetic derived from lactose

A sialyl Lewis X (sLe(x)) mimetic compound, 2-(trimethylsilyl)ethyl 3-O-carboxymethyl-beta-D-galactopyranosyl-(1-->4)-[alpha-L-fucosyl-(1-->6)]-beta-D-glucopyranoside (2a), has been synthesized in 14 steps from D-lactose. This synthesis features the use of the activated glycosylating donor, lactosyl iodide, in a Koenigs-Knorr sequence, the regioselective derivatization at the C-3 position of the galactose moiety, and the stereoselective construction of a fucose-alpha(1-->6)-lactose linkage. The mimetic was tested for its ability to inhibit human polymorphonuclear leukocyte (hPMNL) adhesion to immobilized recombinant human E-selectin under shear stress conditions.     

Detection of carbohydrates using new labeling reagent 1-(2-naphthyl)-3-methyl-5-pyrazolone by capillary zone electrophoresis with absorbance (UV)

Surface plasmon resonance (SPR) was used to screen the interaction between a variety of affinity ligands and hemagglutinin (HA) from human influenza virus, with the aim of identifying low affinity ligands useful for the development of a rapid bioanalytical sensor. Three sialic acid-based structures and four lectins were evaluated as sensor ligands. The sialic acid-based ligands included a natural sialic acid-containing glycoprotein, human alpha1-acid glycoprotein (alpha1-AGP), and two synthetic 6'-sialyllactose-conjugates, with varying degree of substitution. The interaction of HA with the four lectin-based ligands, concanavalin A (Con A), wheat germ agglutinin (WGA), Maackia amurensis lectin (MAL), and Sambucus nigra agglutinin (SNA), showed a wide variation of affinity strengths. Affinity and kinetics data were estimated. Strong affinities were observed for Con A, WGA, alpha1-AGP, and a 6'-sialyllactose-conjugate with a high substitution degree, and low affinities were observed for MAL and a 6'-sialyllactose-conjugate with low substitution. The main objective, to identify a low affinity ligand which could be used for on-line monitoring and product quantification, was met by a 6'-sialyllactose-ovalbumin conjugate that had 0.6 mol ligand per mol carrier protein. The apparent affinity of this ligand was estimated to be 1.5+/-0.03 microM (K(D)) on the SPR surface. Vaccine process samples containing HA were analyzed in the range 10-100 microg HA mL(-1) and correlated with single-radial immunodiffusion. The coefficient of variation on the same chip was between 0.010 and 0.091.     

Synthesis of a sialic acid alpha(2-3) galactose building block and its use in a linear synthesis of sialyl Lewis X

[reaction: see text] The ubiquity of the sialic acid alpha(2-3) galactose linkage in oligosaccharides of biological relevance necessitates a building block for the incorporation of this motif into oligosaccharides prepared by modular synthesis. The linear synthesis of the sialyl Lewis X tumor-associated antigen (1) has been accomplished in good yield using a sialic acid alpha(2-3) galactose disaccharide building block. The disaccharide building block was synthesized efficiently from readily available galactal by a high-yielding and selective sialylation reaction.     

Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein–Ligand Contacts

Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP‐STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D₂O/H₂O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP‐STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket.     

The conformational behaviour and P-selectin inhibition of fluorine-containing sialyl LeX glycomimetics

A combination of experimental J/NOE NMR data with molecular mechanics and dynamics calculations has been used to examine the conformational behaviour and assign the configuration of synthetically prepared epimeric 3-carboxymethyl-O-Gal-(1-->1)-alpha-Man-fluoro-C-glycosides. It is shown that the population distributions around the glycosidic linkages strongly depend on the configuration at the fluorinated carbon of the pseudoacetal residue. It is also shown that these compounds resemble the inhibition ability of sialyl LeX towards P-selectin.     

Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy

The epitope mapping of nucleotides bound to three chromatography supports is accomplished using saturation transfer difference (STD)-NMR spectroscopy. This experiment involves subtracting a spectrum in which the support was selectively saturated from one recorded without support saturation. In the difference spectrum only the signals of the ligands that bind to the support and received saturation transfer remain. The nucleotide protons in closer contact with the support have more intense signals due to a more efficient transfer of saturation. We investigate the effects on the binding to the nucleotides by the introduction of a spacer arm between l-histidine and Sepharose. Our NMR experiments evidence a clear contribution of the spacer to the interaction with all the nucleotides, increasing the mobility of the amino acid and giving different STD responses. This enhanced mobility originates the reinforcement of the interactions with the sugar moiety and phosphate group of 5'-CMP and 5'-TMP or the base of 5'-GMP and 5'-UMP. Hence, with this study we show that by using STD NMR technique on chromatographic systems it is possible to provide a fast, robust and efficient way of screening the atoms involved in the binding to the supports.