Hashem Taha | University of Alberta (original) (raw)
Papers by Hashem Taha
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides
Journal of Chemical Theory and Computation, 2009
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. T... more Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Journal of The American Chemical Society, 2009
A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation ... more A series of investigations probing the mechanism of the 2,3-anhydrosugar migration-glycosylation reaction were performed using a thioglycoside with the D-lyxo stereochemistry as the substrate. Among the work reported are the results of quantum mechanical calculations, NMR studies, the measurement of alpha-deuterium kinetic isotope effects, and the synthesis of a series of substrate analogues. All studies point to a consistent finding: that the reaction proceeds through an oxocarbenium ion intermediate, not an episulfonium ion as previously suggested. It is proposed that the high stereoselectivity of the reaction arises from a preferred "inside attack" of the nucleophile onto the oxocarbenium ion intermediate.
Journal of The American Chemical Society, 2006
Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown... more Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the D-configuration and that they are linked R-(1f4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl R-D-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-R or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-γ and Staphylococcus aureus Cowan strain (SAC/IFN-γ). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.
Journal of The American Chemical Society, 2007
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose... more The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Journal of Chemical Theory and Computation, 2010
A molecular dynamics (MD) investigation on a series of oligo-R-arabinofuranosides