Comparison between DFT- and NMR-based conformational analysis of methyl galactofuranosides

Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).

Conformational preferences of the flexible galactofuranose sugar in gas-phase

In contrast with the predominant pyranose form of galactose, galactofuranose is known to be highly flexible. Such flexibility poses a remarkable challenge in terms of structural studies, thus hindering the in depth understanding of the structure/function relationship in this rare sugar. A thorough computational study based on molecular dynamics and density functional theory supported by vibrational spectroscopy in the gas phase was carried out to provide a better understanding of the instrinsic conformational preferences of galactofuranose. Based on energetic and spectroscopic criteria, we report a subtantially reduced conformational landscape: methyl α-D-galactofuranose adopts E₂/¹E conformations and methyl β-D-galactofuranose adopts ¹T₂/¹E conformations.

The impact of conformational sampling on first-principles calculations of vicinal COCH J-couplings in carbohydrates

Dihedral angles in organic molecules and biomolecules are vital structural parameters that can be indirectly probed by nuclear magnetic resonance (NMR) measurements of vicinal J-couplings. The empirical relations that map the measured couplings to dihedral angles are typically determined by fitting using static structural models, but this neglects the effects of thermal fluctuations at the finite temperature conditions under which NMR measurements are often taken. In this study, we calculate ensemble-averaged J-couplings for several structurally rigid carbohydrate derivatives using first-principles molecular dynamics simulations to sample the thermally accessible conformations around the minimum energy structure. Our results show that including thermal fluctuation effects significantly shifts the predicted couplings relative to single-point calculations at the energy minima, leading to improved agreement with experiments. This provides evidence that accounting for conformational sampling in first-principles calculations can improve the accuracy of NMR-based structure determination for structurally complex carbohydrates.

Computational and NMR Conformational Analysis of Galactofuranoside Cycles Presented in Bacterial and Fungal Polysaccharide Antigens

Unlike pyranoside cycles which are generally characterized by strictly defined conformational preferences, furanosides are flexible and may adopt a wide range of available conformations. During our previous studies, conformational changes of galactofuranoside cycles upon total sulfation were described computationally, using a simple Hartree–Fock (HF) method, and principal conformers of the 5-membered galactose ring were revealed. However, in the case of more complex disaccharide structures, it was found that this method and the widely applied DFT-B3LYP produced results that deviated from experimental evidence. In this study, other DFT functionals (PBE0 and double hybrid B2PLYP) along with RI-MP2 are employed to study the conformational behavior of the galactofuranoside ring. Reinvestigation of galactofuranosides with a lactic acid substituent at O-3 revealed that changes in the orientation of lactic acid residue at O-3 might induce conformational changes of the furanoside cycle. Such findings are important for further modeling of carbohydrate–protein interaction.

Tautomers of N-acetyl-d-allosamine: an NMR and computational chemistry study

d-Allosamine is a rare sugar in Nature but its pyranoid form has been found α-linked in the core region of the lipopolysaccharide from the Gram-negative bacterium Porphyromonas gingivalis and in the chitanase inhibitor allosamidin, then β-linked and N-acetylated. In water solution the monosaccharide N-acetyl-d-allosamine (d-AllNAc) shows a significant presence of four tautomers arising from pyranoid and furanoid ring forms and anomeric configurations. The furanoid ring forms both showed ³J_H1,H2≈ 4.85 Hz and to differentiate the anomeric configurations a series of chemical shift anisotropy/dipole-dipole cross-correlated relaxation NMR experiments was performed in which the α-anomeric form showed notable different relaxation rates for its components of the H1 doublet, thereby making it possible to elucidate the anomeric configuration of each of the furanoses. The conformational preferences of the different forms of d-AllNAc were investigated by ³J_HH, ²J_CH and ³J_CH coupling constants from NMR experiments, molecular dynamics simulations and density functional theory calculations. The pyranose form resides in the ⁴C₁ conformation and the furanose ring form has the majority of its conformers located on the South-East region of the pseudorotation wheel, with a small population in the Northern hemisphere. The tautomeric equilibrium was quite sensitive to changes in temperature, where the β-anomer of the pyranoid ring form decreased upon a temperature increase while the other forms increased.

Distinguishing Galactoside Isomers with Mass Spectrometry and Gas-Phase Infrared Spectroscopy

Sequencing glycans is demanding due to their structural diversity. Compared to mammalian glycans, bacterial glycans pose a steeper challenge because they are constructed from a larger pool of monosaccharide building blocks, including pyranose and furanose isomers. Though mammalian glycans incorporate only the pyranose form of galactose (Galp), many pathogens, including Mycobacterium tuberculosis and Klebsiella pneumoniae, contain galactofuranose (Galf) residues in their cell envelope. Thus, glycan sequencing would benefit from methods to distinguish between pyranose and furanose isomers of different anomeric configurations. We used infrared multiple photon dissociation (IRMPD) spectroscopy with mass spectrometry (MS-IR) to differentiate between pyranose- and furanose-linked galactose residues. These targets pose a challenge for MS-IR because the saccharides lack basic groups, and galactofuranose residues are highly flexible. We postulated cationic groups that could complex through hydrogen bonding would offer a solution. Here, we present the first MS-IR analysis of hexose ammonium adducts. We compared their IR fingerprints with those of lithium adducts. We determined the diagnostic MS-IR signatures of the α- and β-anomers of galactose in furanose and pyranose forms. We also showed these signatures could be applied to disaccharides to assign galactose ring size. Our findings highlight the utility of MS-IR for analyzing the unique substructures that occur in bacterial glycans.

Synthesis of an Exhaustive Library of Naturally Occurring Galf-Manp and Galp-Manp Disaccharides. Toward Fingerprinting According to Ring Size by Advanced Mass Spectrometry-Based IM-MS and IRMPD

Nature offers a huge diversity of glycosidic derivatives. Among numerous structural modulations, the nature of the ring size of hexosides may induce significant differences on both biological and physicochemical properties of the glycoconjugate of interest. On this assumption, we expect that small disaccharides bearing either a furanosyl entity or a pyranosyl residue would give a specific signature, even in the gas phase. On the basis of the scope of mass spectrometry, two analytical techniques to register those signatures were considered, i.e., the ion mobility (IM) and the infrared multiple photon dissociation (IRMPD), in order to build up cross-linked databases. d-Galactose occurs in natural products in both tautomeric forms and presents all possible regioisomers when linked to d-mannose. Consequently, the four reducing Galf-Manp disaccharides as well as the four Galp-Manp counterparts were first synthesized according to a highly convergent approach, and IM-MS and IRMPD-MS data were second collected. Both techniques used afforded signatures, specific to the nature of the connectivity between the two glycosyl entities.

Synthesis and conformational analysis of vicinally branched trisaccharide β-d-Galf-(1 → 2)-[β-d-Galf-(1 → 3)-]-α-Galp from Cryptococcus neoformans galactoxylomannan

The synthesis of a vicinally branched trisaccharide composed of two d-galactofuranoside residues attached viaβ-(1 → 2)- and β-(1 → 3)-linkages to the α-d-galactopyranoside unit has been performed for the first time. The reported trisaccharide represents the galactoxylomannan moiety first described in 2017, which is the capsular polysaccharide of the opportunistic fungal pathogen Cryptococcus neoformans responsible for life-threatening infections in immunocompromised patients. The NMR-data reported here for the synthetic model trisaccharide are in good agreement with the previously assessed structure of galactoxylomannan and are useful for structural analysis of related polysaccharides. The target trisaccharide as well as the constituent disaccharides were analyzed by a combination of computational and NMR methods to demonstrate good convergence of the theoretical and experimental results. The results suggest that the furanoside ring conformation may strongly depend on the aglycon structure. The reported conformational tendencies are important for further analysis of carbohydrate-protein interaction, which is critical for the host response toward C. neoformans infection.

Theoretical and practical study of the cefoxitin-Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria

The penicillin-binding proteins (PBPs) are important biological target for new antibacterial drugs development. This study focused on molecular interaction between cefoxitin and the Escherichia coli PBP5 by molecular dynamics (MD) using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations approach, searching to develop a computational simulations prototype method on antimicrobial susceptibility of gram-negative bacteria against antibiotics. Escherichia coliATCC 8739 strain susceptibility for the drugs used in the antimicrobial susceptibility testing and selection of bioactive molecules against resistant strain. The protonation revealed a deprotonate state for His146, His151, His216, and His320 residues. The complex was stabilized after 0.6 ns of MD simulation. The global interaction means for inhibition zone diameters of E. coliATCC8739 strain and cefoxitin were 24.33 mm no showing significant difference between computational and experimental methods. Our computational simulation method can reliably be performed as a molecular modeling prototype for gram-negative antimicrobial susceptibility testing bacteria.

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

The studies on the recently discovered pyranoside-into-furanoside rearrangement have led us to conformational investigations of furanosides upon their total sulfation. Experimental NMR data showed that in some cases drastic changes of the ring conformation occurred while sometimes only the conformation of the exocyclic C4-C5 linkage changed. Herein we describe a combined quantum chemical and NMR conformational investigation of three common monosaccharide furanosides as their propyl glycosides: α-mannose, β-glucose and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4-H5 protons in the non-sulfated molecules which changed to gauche-orientation upon sulfation. The effect is less pronounced in the galactosides. For all the studied structures changes in the conformational distribution were revealed by quantum mechanical calculations, that explained the observed changes in intraring coupling constants occurring upon introduction of sulfates.

Spectroscopic diagnostic for the ring-size of carbohydrates in the gas phase: furanose and pyranose forms of GalNAc

Hexoses are sparingly found in nature in the furanose form (5-membered ring).

Enzymatic Synthesis of GDP-α-l-fucofuranose by MtdL and Hyg20

Two mutases, MtdL and Hyg20, are reported. Both are able to functionally drive the biosynthesis of GDP-α-l-fucofuranose. Both enzymes catalyze similar functions, catalytically enabling the bidirectional reaction between GDP-β-l-fucopyranose and GDP-α-l-fucofuranose using only divalent cations as cofactors. This realization is but one of a number of important insights into fucofuranose biosynthesis presented herein.

Threocytidines: Insight into the Conformational Preferences of Artificial Threose Nucleic Acid (TNA) Building Blocks in B3LYP Studies

A systematic DFT conformational studies of four building blocks of TNA with cytosine attached to the C1' atom of the α-L-threofuranose moiety are presented. Structures bearing 2'-OR and 3'-OR substituents, where R represents H, CH₃ and phosphate groups, were used in the studies using a B3LYP functional in the gas phase. The χ angle (C2-N1-C1'-O4'), the ν₀-ν₄ endocyclic torsion angles and the exocyclic torsion angles ε (X-O2'-C2'-C1') and γ (X-O3'-C3'-C2') geometry parameter variations were taken into consideration. Three energy minima, high-anti, anti and syn, were found for the rotation about the C1'-N1 bond. The high-anti orientation of the base with respect to the sugar moiety, turned out to be preferred, regardless of the substituents at the C2' and C3' positions. Other orientations are at least 1.65 kcal/mol higher in Gibbs free energy than the high-anti one. It has been shown that intramolecular H-bonds and the anomeric effect of phosphate groups strongly affect the conformational preferences of the studied compounds. Further, the structure of substituents attached to the sugar moiety influence the pucker of the furanoid ring. The furanoid ring in the global minima of the compound with two OH groups (TC1) in the 2' and 3' positions, and the compound having a 3'-phosphate group (TC2), adopt roughly the same conformation located at the southern range of the pseudorotation wheel, and thus are close to those found in the B type DNA helix. The low-energy high-anti rotamers of the geometry with the phosphate group attached to the sugar ring in the 2' position (TC3) and the geometry with two methoxyl groups (TC4) have their furanoid rings in conformations resembling those found in A DNA and RNA helices (the northern range of the pseudorotation wheel).

Conformational studies of N-(α-d-glucofuranurono-6,3-lactone)- and N-(methyl β-d-glucopyranuronate)-p-nitroanilines

N-(α-d-Glucofuranurono-6,3-lactone)-p-nitroaniline and N-(methyl β-d-glucopyranuronate)-p-nitroaniline were obtained as crystalline solids. The single-crystal X-ray diffraction, NMR data and DFT calculations for N-(α-d-glucofuranurono-6,3-lactone)-p-nitroaniline indicate that this N-furanoside adopts a ³T₂/³E-like conformation in the crystal lattice, solution and gas phase. Thus, the structure of recorded for N-furanoside ¹H NMR spectrum is indicative of the ³T₂/³E region of the pseudorotational itinerary for furanose derivatives with α-d-gluco, β-L-ido and α-d-xylo configurations. Moreover, it is concluded that the ¹T₂/E₂/³T₂/³E region of the pseudorotational itinerary for furanose derivatives with d-gluco, L-ido and d-xylo configurations should be characterised by the lack of coupling between H2 and H3 protons, irrespective of the anomeric configuration. Such a lack of vicinal coupling is characteristic for some of the trans-oriented furanose ring protons. The single-crystal X-ray diffraction and NMR data for N-(methyl β-d-glucopyranuronate)-p-nitroaniline indicate that this N-glucuronide adopts the ⁴C₁ conformation, both in the crystal lattice and solution. The occurrence of anomeric effects in the presented N-glycosides is discussed. The crystal structure analysis of both N-glycosides gives evidence that the amine group in p-nitroaniline is planar due to the nitrogen sp² hybridisation.

Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase

Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Galp), or as a five-membered ring, galactofuranose (Galf). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Galf Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Galf production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: (i) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and (ii) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Galf-containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies.

Synthesis and Evaluation of Bicyclo[3.1.0]hexane-Based UDP-Galf Analogues as Inhibitors of the Mycobacterial Galactofuranosyltransferase GlfT2

UDP-galactofuranose (UDP-Galf) is the donor substrate for both bifunctional galactofuranosyltransferases, GlfT1 and GlfT2, which are involved in the biosynthesis of mycobacterial galactan. In this paper, a group of UDP-Galf mimics were synthesized via reductive amination of a bicyclo[3.1.0]hexane-based amine by reacting with aromatic, linear, or uridine-containing aldehydes. These compounds were evaluated against GlfT2 using a coupled spectrophotometric assay, and were shown to be weak inhibitors of the enzyme.

Insights into furanose solution conformations: beyond the two-state model

A two-state model is commonly used for interpreting ring conformations of furanoses based on NMR scalar (3) J-coupling constants, with the ring populating relatively narrow distributions in the North and the South of the pseudorotation itinerary. The validity of this simple approach has been questioned, and is examined here in detail employing molecular dynamics (MD) simulations with a new GLYCAM force field parameter set for furanoses. Theoretical (3) J-coupling constants derived from unrestrained MD simulations with the new furanose-specific parameters agreed with the experimental coupling constants to within 1 Hz on average. The results confirm that a two state model is a reasonable description for the ring conformation in the majority of methyl furanosides. However, in the case of methyl α-D-arabinofuranoside the ring populates a continuum of states from North to South via the eastern side of the pseudorotational itinerary. Two key properties are responsible for these differences. Firstly, East and West regions in β- and α-anomers, respectively, are destabilized by the absence of the anomeric effect. And, secondly, East or West conformations can be further destabilized by repulsive interactions among vicinal hydroxyl groups and ring oxygen atoms when the vicinal hydroxyl groups are in syn-configurations (such as in ribose and lyxose) more so than when in anti (arabinose, xylose).

Recognition of microbial glycans by human intelectin-1

The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. We used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol-modified glycans, heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO). The 1.6-Å-resolution crystal structure of hIntL-1 complexed with β-Galf revealed that hIntL-1 uses a bound calcium ion to coordinate terminal exocyclic 1,2-diols. N-acetylneuraminic acid (Neu5Ac), a sialic acid widespread in human glycans, has an exocyclic 1,2-diol but does not bind hIntL-1, probably owing to unfavorable steric and electronic effects. hIntL-1 marks only Streptococcus pneumoniae serotypes that display surface glycans with terminal 1,2-diol groups. This ligand selectivity suggests that hIntL-1 functions in microbial surveillance.

Novel sulfated phosphoglycolipids from Natronomonas moolapensis

Polar lipid pattern determination is often used for the taxonomic classification of halophilic Archaea in addition to a genomic characterization. During the analysis of polar lipid extracts from the recently described haloarchaeon Natrononomonas moolapensis, an unknown glycolipid was detected. Fragmentation patterns observed from preliminary mass spectrometric analysis initially suggested the presence of a sulfo-hexosyl-phosphatidylglycerol. However, by NMR spectroscopy and enzymatic assays the existence of two isomeric molecules with different hexoses (1-(6-sulfo-d-glcp/galf-β1,2-glycero)-phospho-2,3-diphytanylglycerol) could be shown. The structural origin from phosphatidylglycerol distinguishes these glycolipids within Archaea, because all other characterized haloarchaeal glycolipids consist of diphytanylglycerol directly linked to an oligoglycosyl moiety. Now the door is open to investigate the physical and functional consequences of these architectural differences of the head groups.

Quinofuracins A-E, produced by the fungus Staphylotrichum boninense PF1444, show p53-dependent growth suppression

Quinofuracins A-E, novel anthraquinone derivatives containing β-D-galactofuranose that were isolated from the fungus Staphylotrichum boninense PF1444, induced p53-dependent cell death in human tumor cells. The structures of quinofuracins A-E, including absolute configurations, were elucidated by extensive spectroscopic analysis and chemical transformation studies. Quinofuracins were classified into three groups according to the aglycone moieties. 5'-Oxoaverantin was present in quinofuracins A-C, whereas averantin and versicolorin B were identified in quinofuracins D and E, respectively. These quinofuracins induced p53-dependent growth suppression in human glioblastoma LNZTA3 cells.

Specificity of furanoside-protein recognition through antibody engineering and molecular modeling

Recognition of furanosides (five-membered ring sugars) by proteins plays important roles in host-pathogen interactions. In comparison to their six-membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in-depth molecular characterization of a furanoside-protein interaction system, between an antibody (CS-35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS-35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH-π interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries.