Developments in the Karplus equation as they relate to the NMR coupling constants of carbohydrates

Insights into the stereoisomerism of dihydroquercetin: analytical and pharmacological aspects

Dihydroquercetin (DHQ) is a representative of flavonoids that is available on the market as a food supplement and registered as an active pharmaceutical ingredient. The structure of this compound is characterized by the presence of two chiral centers in positions 2 and 3 of the pyranone ring. Current regulatory documentation on DHQ lacks quantitative analysis of the stereoisomers of this flavanonol. This poses potential risks for consumers of DHQ-based dietary supplements and developers of new drugs. This review was conducted to systematize data on the pharmacology of DHQ stereoisomers and the possible methods of controlling them in promising chiral drugs. We found that relying on literature data of polarimetry for the identification of DHQ stereoisomers is currently impossible due to these heterogeneities. NMR spectroscopy allows to distinguishing between trans- and cis-DHQ using chemical shifts values. Only HPLC is currently characterized by sufficient enantioselectivity. Regarding pharmacology, the most active stereoisomer of DHQ should be identified, if the substituents in chiral centers both take part in binding with the biological target. The significant impact of stereochemical structure on the pharmacokinetics of DHQ isomers was reported. The question about these toxicity of these compounds remains open. The results of the conducted review of scientific literature indicate the necessity of revising the pharmacology of DHQ taking into account its stereoisomerism.

One-Step Synthesis, Crystallography, and Acute Toxicity of Two Boron-Carbohydrate Adducts That Induce Sedation in Mice

Boronic acids form diester bonds with cis-hydroxyl groups in carbohydrates. The formation of these adducts could impair the physical and chemical properties of precursors, even their biological activity. Two carbohydrate derivatives from d-fructose and d-arabinose and phenylboronic acid were synthesized in a straightforward one-step procedure and chemically characterized via spectroscopy and X-ray diffraction crystallography. Additionally, an acute toxicity test was performed to determine their lethal dose 50 (LD50) values by using Lorke's method. Analytical chemistry assays confirmed the formation of adducts by the generation of diester bonds with the β-d-pyranose of carbohydrates, including signals corresponding to the formation of new bonds, such as the stretching of B-O bonds. NMR spectra yielded information about the stereoselectivity in the synthesis reaction: Just one signal was found in the range for the anomeric carbon in the 13C NMR spectra of both adducts. The acute toxicity tests showed that the LD50 value for both compounds was 1265 mg/kg, while the effective dose 50 (ED50) for sedation was 531 mg/kg. However, differences were found in the onset and lapse of sedation. For example, the arabinose derivative induced sedation for more than 48 h at 600 mg/kg, while the fructose derivative induced sedation for less than 6 h at the same dose without the death of the mice. Thus, we report for the first time two boron-containing carbohydrate derivatives inducing sedation after intraperitoneal administration. They are bioactive and highly safe agents. Further biological evaluation is desirable to explore their medical applications.

NMR-Verified Dearomatization of 5,7-Substituted Pyrazolo[1,5-a]pyrimidines

Tetrahydropyrazolo[1,5-a]pyrimidine (THPP) is an attractive scaffold for designing biologically active compounds. The most obvious way to obtain such compounds is to reduce pyrazolopyrimidines with complex hydrides, because the pyrimidine ring is reduced in the preference over the pyrazole ring. The presence of substituents at positions five and seven of pyrazolo[1,5-a]pyrimidines complicates the set of reaction products but makes it more attractive for medicinal chemistry because four possible stereoisomers can be formed during reduction. However, the formation of only syn-isomers has been described in the literature. This article is the first report on the formation of anti-configured isomers along with syn-isomers in the reduction of model 5,7-dimethylpyrazolo[1,5-a]pyrimidine, which was confirmed by NMR. The bicyclic core in the syn-configuration was shown to be conformationally stable, which was used to estimate the long-range interproton distances using NOESY data. At the same time, long-range dipole-dipole interactions corresponding to a distance between protons of more than 6 Å were first registered and quantified. In turn, the bicyclic core in the trans-configuration represents a conformationally labile system. For these structures, an analysis of conformations observed in solutions was carried out. Our results indicate the significant potential of trans-configured tetrahydropyrazolo[1,5-a]pyrimidines for the development of active small molecules. While possessing structural lability due to the low energy of the conformational transition, they have the ability to adjust to the active site of the desired target.

Linking the Interatomic Exchange-Correlation Energy to Experimental J-Coupling Constants

The main aim of the current work is to find an experimental connection to the interatomic exchange-correlation energy as defined by the energy decomposition method Interacting Quantum Atoms (IQA). A suitable candidate as (essentially) experimental quantity is the nuclear magnetic resonance (NMR) J-coupling constant denoted ³J(H,H'), which a number of previous studies showed to correlate well with QTAIM's delocalization index (DI), which is essentially a bond order. Inspired by Karplus equations, here, we investigate correlations between ³J(H,H') and a relevant dihedral angle in six simple initial compounds of the shape H₃C-YH_n (Y = C, N, O, Si, P, and S), N-methylacetamide (as prototype of the peptide bond), and five peptide-capped amino acids (Gly, Ala, Val, Ile, and Leu) because of the protein direction of the force field FFLUX. In conclusion, except for methanol, the inter-hydrogen exchange-correlation energy V_xc(H,H') makes the best contact with experiment, through ³J(H,H'), when multiplied with the internuclear distance R_HH'.

Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides

To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.

Investigation of the influence of chirality and halogen atoms on the anticancer activity of enantiopure palladium(ii) complexes derived from chiral amino-alcohol Schiff bases and 2-picolylamine

In order to evaluate the impact of chirality and halogen-substitution pattern on biological activity, four mixed-ligand enantiomeric pairs of Pd(ii) complexes were synthesized and characterized.

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity

Activation entropy (ΔS ^‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ^‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ^‡ of 16.02 cal·mol^-1·K^-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

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.

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic

O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at -10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.

Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy

3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond ¹H,¹³C residual dipolar couplings (RDCs) or by ¹³C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of ¹³C preventing their use for compounds available only in quantities of a few 10’s of µgs. By contrast, ¹H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant ¹H spin. Herein, ¹H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum.

Determination of 3D molecular structures remains challenging for natural products or organic compounds available in minute amounts. Here, the authors determine the structure of complex molecules, including few micrograms of briarane B-3 isolated from Briareum asbestinums, through measurement of ¹H residual chemical shift anisotropy.

How large a 3 JHCCH coupling can be? Prediction of giant vicinal couplings in quinonoid systems

Second-order polarization propagator approximation (SOPPA) and density functional theory (DFT) B3LYP computations revealed the presence of giant ³ J_HCCH couplings, up to more than 60 Hz, in conjugated quinonoid systems, very far above the typical limit of ~15 Hz. Strong hyperconjugative interactions of the C-H σ orbitals with the quinonoid 8-e^- π system, which allows effective propagation of the spin polarization, seem to be responsible for those extraordinarily large couplings. Computation on several model systems showed the additive nature of the contributions from the available coupling paths to the total coupling.

Synthetic Approaches to Phosphasugars (2-oxo-1,2-oxaphosphacyclanes) Using the Anomeric Alkoxyl Radical β-Fragmentation Reaction as the Key Step

The anomeric alkoxyl radical β-fragmentation (ARF) of carbohydrates possessing an electron-withdrawing group (EWG) at C2, promoted by PhI(OAc)₂/I₂, gives rise to an acyclic iodide through which a pentavalent atom of phosphorus can be introduced via the Arbuzov reaction. After selective hydrolysis and subsequent cyclization, the phosphonate or phosphinate intermediates can be converted into 2-deoxy-1-phosphahexopyranose and 2-deoxy-1-phosphapentopyranose sugars. The ARF of carbohydrates with an electron-donor group (EDG) at C2 proceeds by a radical-polar crossover mechanism, and the cyclization occurs by nucleophilic attack of a conveniently positioned phosphonate or phosphinate group to the transient oxocarbenium ion. This alternative methodology leads to 5-phosphasugars with a 4-deoxy-5-phosphapentopyranose framework. The structure and conformation of the 2-oxo-1,2-oxaphosphinane and 2-oxo-1,2-oxaphospholane ring systems in different carbohydrate models have been studied by NMR and X-ray crystallography.

IMPRESSION - prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy

The IMPRESSION (Intelligent Machine PREdiction of Shift and Scalar information Of Nuclei) machine learning system provides an efficient and accurate method for the prediction of NMR parameters from 3-dimensional molecular structures. Here we demonstrate that machine learning predictions of NMR parameters, trained on quantum chemical computed values, can be as accurate as, but computationally much more efficient (tens of milliseconds per molecular structure) than, quantum chemical calculations (hours/days per molecular structure) starting from the same 3-dimensional structure. Training the machine learning system on quantum chemical predictions, rather than experimental data, circumvents the need for the existence of large, structurally diverse, error-free experimental databases and makes IMPRESSION applicable to solving 3-dimensional problems such as molecular conformation and stereoisomerism.

Combining pure shift and J-edited spectroscopies: A strategy for extracting chemical shifts and scalar couplings from highly crowded proton spectra of oligomeric saccharides

We report the application of pure shift and J-edited nuclear magnetic resonance spectroscopies to the structural analysis of a protected maltotrioside synthetic intermediate whose crowded ¹ H spectrum displays highly crowded regions. The analytical strategy is based on the implementation of J-edited and TOCSY experiments whose resolution is optimized by the use of broadband homonuclear decoupling and selective refocusing techniques, to assign and measure chemical shifts and homonuclear scalar couplings with high accuracy. The resulting data show a high level of complementarity, providing a detailed insight into each subunit of this oligomeric saccharide, even for proton sites whose nuclear magnetic resonance signals strongly overlap. This approach allowed for fully assigning proton chemical shifts and extracting 80% of the ³ J_HH couplings that are in excellent agreement with those expected for D-gluco-pyranosyl units in ⁴ C₁ conformations.

Interplay of Protecting Groups and Side Chain Conformation in Glycopyranosides. Modulation of the Influence of Remote Substituents on Glycosylation?

The synthesis and conformational analysis of a series of phenyl 2,3,6-tri-O-benzyl-β-d-thio galacto- and glucopyranosides and their 6S-deuterio isotopomers, with systematic variation of the protecting group at the 4-position, are described. For the galactopyranosides, replacement of a 4-O-benzyl ether by a 4-O-alkanoyl or aroyl ester results in a small but measurable shift in side chain population away from the trans,gauche conformation and in favor of the gauche,trans conformer. In the glucopyranoside series on the other hand, replacement of a 4-O-benzyl ether by a 4-O-alkanoyl or aroyl ester results in a small but measurable increase in the population of the trans,gauche conformer at the expense of the gauche,gauche conformer. The possible modulating effect of these conformational changes on the well-known changes in the anomeric reactivity of glycosyl donors as a function of protecting group is discussed, raising the possibility that larger changes may be observed at the transition state for glycosylation. A comparable study with a series of ethyl 2,3,4-tri-O-benzyl-β-d-thioglucopyranosides reveals that no significant influence in side chain population is observed on changing the O6 protecting group.

Predicting the Structures of Glycans, Glycoproteins, and Their Complexes

Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.

Synthesis of Conformationally-Locked cis- and trans-Bicyclo[4.4.0] Mono-, Di-, and Trioxadecane Modifications of Galacto- and Glucopyranose; Experimental Limiting 3JH,H Coupling Constants for the Estimation of Carbohydrate Side Chain Populations and Beyond

Hexopyranose side chains populate three staggered conformations, whose proportions can be determined from the three sets of ideal limiting 3JH5,H6R and 3JH5,H6S coupling constants in combination with the time-averaged experimental coupling constants. Literature values for the limiting coupling constants, obtained by the study of model compounds, the use of the Haasnoot-Altona and related equations, or quantum mechanical computations, can result in computed negative populations of one of the three ideal conformations. Such values arise from errors in the limiting coupling constants and/or from the population of nonideal conformers. We describe the synthesis and analysis of a series of cis- and trans-fused mono-, di-, and trioxabicyclo[4.4.0]octane-like compounds. Correction factors for the application of data from internal models (-CH(OR)-CH(OR)-) to terminal systems (-CH(OR)-CH2(OR)) are deduced from comparison of further models, and applied where necessary. Limiting coupling constants so-derived are applied to the side chain conformations of three model hexopyranosides, resulting in calculated conformer populations without negative values. Although, developed primarily for hexopyranose side chains, the limiting coupling constants are suitable, with the correction factors presented, for application to the side chains of higher carbon sugars and to conformation analysis of acyclic diols and their derivatives in a more general sense.

Theoretical and NMR-based Conformational Analysis of Phosphodiester-linked Disaccharides

The conformational behaviour of three phosphate-bridged dimannosides was studied by means of NMR and computational molecular modelling. First, the conformations of the phosphodiester linker were determined by quantum chemistry methods using dimethyl phosphate as a model. Then, a series of conformations was constructed for each of the studied molecules. Preliminary molecular dynamics (MD) simulations revealed that the inclusion of a cation had a drastic influence on the obtained results. Additionally, triethylammonium had the same effect as sodium as the counter-ion. After that, another series of MD simulations was run. The resulting MD trajectories were used to define the conformations responsible for the observed nuclear Overhauser effects and inter-nuclear coupling.

Biosynthesis of natural and non-natural genistein glycosides

Biosynthesis of various genistein glycopyranoside scaffolds using versatile GTs and SOMTs. Each compound was structurally characterized and biological activity assay was carried out.

Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions

The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

Conformational analysis: ³JHCOC and ³JHCCC Karplus relationships for methylene ¹H nuclei

NAMFIS (NMR Analysis of Molecular Flexibility In Solution) was applied to 1-[2-(benzyloxy)phenyl]ethanone using quantitative (1)H-(1)H NOE distances and (3)J proton-carbon coupling constant (CC) restraints for averaged methylene proton (3)J(HCOC) and (3)J(HCCC) pathways H2-(3)J-X imposed by density functional theory-generated Karplus relationships. Comparison of the NOE-only versus the NOE + CC conformational selections illustrates that the experimentally measured average (3)J coupling constants of methylene protons can be used for solution conformational analysis, potentially valuable in the study of small-molecule drugs and natural products which lack the typically studied H1-(3)J-X Karplus relationships.

Development of αGlcN(1↔1)αMan-based lipid A mimetics as a novel class of potent Toll-like receptor 4 agonists

The endotoxic portion of lipopolysaccharide (LPS), a glycophospholipid Lipid A, initiates the activation of the Toll-like Receptor 4 (TLR4)–myeloid differentiation factor 2 (MD-2) complex, which results in pro-inflammatory immune signaling. To unveil the structural requirements for TLR4·MD-2-specific ligands, we have developed conformationally restricted Lipid A mimetics wherein the flexible βGlcN(1→6)GlcN backbone of Lipid A is exchanged for a rigid trehalose-like αGlcN(1↔1)αMan scaffold resembling the molecular shape of TLR4·MD-2-bound E. coli Lipid A disclosed in the X-ray structure. A convergent synthetic route toward orthogonally protected αGlcN(1↔1)αMan disaccharide has been elaborated. The α,α-(1↔1) linkage was attained by the glycosylation of 2-N-carbamate-protected α-GlcN-lactol with N-phenyl-trifluoroacetimidate of 2-O-methylated mannose. Regioselective acylation with (R)-3-acyloxyacyl fatty acids and successive phosphorylation followed by global deprotection afforded bis- and monophosphorylated hexaacylated Lipid A mimetics. αGlcN(1↔1)αMan-based Lipid A mimetics (α,α-GM-LAM) induced potent activation of NF-κB signaling in hTLR4/hMD-2/CD14-transfected HEK293 cells and robust LPS-like cytokines expression in macrophages and dendritic cells. Thus, restricting the conformational flexibility of Lipid A by fixing the molecular shape of its carbohydrate backbone in the “agonistic” conformation attained by a rigid αGlcN(1↔1)αMan scaffold represents an efficient approach toward powerful and adjustable TLR4 activation.

NMR of glycans: shedding new light on old problems

The diversity in molecular arrangements and dynamics displayed by glycans renders traditional NMR strategies, employed for proteins and nucleic acids, insufficient. Because of the unique properties of glycans, structural studies often require the adoption of a different repertoire of tailor-made experiments and protocols. We present an account of recent developments in NMR techniques that will deepen our understanding of structure-function relations in glycans. We open with a survey and comparison of methods utilized to determine the structure of proteins, nucleic acids and carbohydrates. Next, we discuss the structural information obtained from traditional NMR techniques like chemical shifts, NOEs/ROEs, and coupling-constants, along with the limitations imposed by the unique intrinsic characteristics of glycan structure on these approaches: flexibility, range of conformers, signal overlap, and non-first-order scalar (strong) coupling. Novel experiments taking advantage of isotopic labeling are presented as an option for overcoming spectral overlap and raising sensitivity. Computational tools used to explore conformational averaging in conjunction with NMR parameters are described. In addition, recent developments in hydroxyl detection and hydrogen bond detection in protonated solvents, in contrast to traditional sample preparations in D2O for carbohydrates, further increase the tools available for both structure information and chemical shift assignments. We also include previously unpublished data in this context. Accurate determination of couplings in carbohydrates has been historically challenging due to the common presence of strong-couplings. We present new strategies proposed for dealing with their influence on NMR signals. We close with a discussion of residual dipolar couplings (RDCs) and the advantages of using (13)C isotope labeling that allows gathering one-bond (13)C-(13)C couplings with a recently improved constant-time COSY technique, in addition to the commonly measured (1)H-(13)C RDCs.

1H NMR spectra of butane-1,4-diol and other 1,4-diols: DFT calculation of shifts and coupling constants

The proton nuclear magnetic resonance (NMR) spectra of butane-1,4-diol, pentane-1,4-diol, (S,S)-hexane-2,5-diol, 2,5-dimethylhexane-2,5-diol and cyclohexane-1,4-diols (cis and trans) in benzene and some other solvents have been analysed. The conformer distribution and the NMR shifts of these diols in benzene have been computed on the basis of the density functional theory, the solvent being included by means of the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. Vicinal three-bond coupling constants for the acyclic diols are calculated from the relative conformer populations, the geometries and generalized Karplus equations developed by Altona's group; these correlate well with the experimental values. The solvent dependence of coupling constants for butane-1,4-diol is attributed to conformational change. Coupling constants for the rigid cyclohexane-1,4-diols do not change with solvent and are readily explained in terms of their geometries. The NMR shifts of hydrogen-bonded protons in individual conformers of alkane-1,n-diols show a very rough correlation with the OH · · · OH distances. The computed overall NMR shifts for CH protons in 1,2-diols, 1,3-diols and 1,4-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01; those for OH protons correlate less well.

Long-range proton-carbon coupling constants: NMR methods and applications

A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.

A perspective on the primary and three-dimensional structures of carbohydrates

Carbohydrates, in more biologically oriented areas referred to as glycans, constitute one of the four groups of biomolecules. The glycans, often present as glycoproteins or glycolipids, form highly complex structures. In mammals ten monosaccharides are utilized in building glycoconjugates in the form of oligo- (up to about a dozen monomers) and polysaccharides. Subsequent modifications and additions create a large number of different compounds. In bacteria, more than a hundred monosaccharides have been reported to be constituents of lipopolysaccharides, capsular polysaccharides, and exopolysaccharides. Thus, the number of polysaccharide structures possible to create is huge. NMR spectroscopy plays an essential part in elucidating the primary structure, that is, monosaccharide identity and ring size, anomeric configuration, linkage position, and sequence, of the sugar residues. The structural studies may also employ computational approaches for NMR chemical shift predictions (CASPER program). Once the components and sequence of sugar residues have been unraveled, the three-dimensional arrangement of the sugar residues relative to each other (conformation), their flexibility (transitions between and populations of conformational states), together with the dynamics (timescales) should be addressed. To shed light on these aspects we have utilized a combination of experimental liquid state NMR techniques together with molecular dynamics simulations. For the latter a molecular mechanics force field such as our CHARMM-based PARM22/SU01 has been used. The experimental NMR parameters acquired are typically (1)H,(1)H cross-relaxation rates (related to NOEs), (3)JCH and (3)JCCtrans-glycosidic coupling constants and (1)H,(13)C- and (1)H,(1)H-residual dipolar couplings. At a glycosidic linkage two torsion angles ϕ and ψ are defined and for 6-substituted residues also the ω torsion angle is required. Major conformers can be identified for which highly populated states are present. Thus, in many cases a well-defined albeit not rigid structure can be identified. However, on longer timescales, oligosaccharides must be considered as highly flexible molecules since also anti-conformations have been shown to exist with H-C-O-C torsion angles of ∼180°, compared to syn-conformations in which the protons at the carbon atoms forming the glycosidic linkage are in close proximity. The accessible conformational space governs possible interactions with proteins and both minor changes and significant alterations occur for the oligosaccharides in these interaction processes. Transferred NOE NMR experiments give information on the conformation of the glycan ligand when bound to the proteins whereas saturation transfer difference NMR experiments report on the carbohydrate part in contact with the protein. It is anticipated that the subtle differences in conformational preferences for glycan structures facilitate a means to regulate biochemical processes in different environments. Further developments in the analysis of glycan structure and in particular its role in interactions with other molecules, will lead to clarifications of the importance of structure in biochemical regulation processes essential to health and disease.

Measurement and applications of long-range heteronuclear scalar couplings: recent experimental and theoretical developments

The use of long-range heteronuclear couplings, in association with (1)H-(1)H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long-range homo- and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J-couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short- and long-range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long-range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium- to larger-sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.

Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations

The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-L-Fucp-(1 → 2)-β-D-Galp-(1 → 3)-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τ(N), was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τ(M), of ∼0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, τ(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of ∼30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.

Acid epimerization of 20-keto pregnane glycosides is determined by 2D-NMR spectroscopy

Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution (1)H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as starting points in several selective NMR experiments to study scalar (J coupling), and dipolar (NOE) interactions. ROESY is especially suited for molecules such that ωτ(c) ~ 1, where τ(c) are the motional correlation times and ω is the angular frequency. In these cases the NOE is nearly zero, while the rotating-frame Overhauser effect spectroscopy (ROESY) is always positive and increases monotonically for increasing values of τ(c). The ROESY shows dipolar interactions cross peaks even in medium-sized molecules which are helpful in unambiguous assignment of all the interglycosidic linkages. Selective excitation was carried out using a double pulsed-field gradient spin-echo sequence (DPFGSE) in which 180° Gaussian pulses are sandwiched between sine shaped z-gradients. Scalar interactions were studied by homonuclear DPFGSE-COSY and DPFGSE-TOCSY experiments, while DPFGSE-ROESY was used to monitor the spatial environment of the selectively excited proton. Dipolar interactions between nuclei close in space can be detected by the 1D GROESY experiment, which is a one-dimensional counterpart of the 2D ROESY method. The C-12 and C-17 configurations were determined by ROESY experiments.

The conformation of tetrafluorinated methyl galactoside anomers: crystallographic and NMR studies

The first single-crystal X-ray diffraction study of tetrafluorinated monosaccharide derivatives is presented. Both α- and β-methyl 2,3-dideoxy-2,2,3,3-tetrafluoro-d-galactopyranoside anomers adopt the (4)C(1) conformation. The values for the C1-O1 and C1-O5 bond lengths and the O5-C1-O1-CH(3) dihedral angles are in line with what can be expected from the anomeric and exo-anomeric effects. The chair conformations are slightly distorted, presumably due to repulsion between 1,3-diaxial C-O and C-F bonds. The asymmetric unit of both compounds contains up to three independent molecules, which differ in the conformation of the hydroxymethyl group (including in one case a 'forbidden'gg rotamer). The molecular packing of the β-anomer shows a clear segregation between fluorinated and hydrophilic domains, while for the α-anomer the regions of fluorine segregation are broken by interleafing of OMe groups. There is one close OH⋯F contact, which is likely to arise from the crystal packing. NMR studies show that the two anomers also adopt a (4)C(1) conformation in solution (D(2)O, CDCl(3)).

The structure of the Escherichia coli O148 lipopolysaccharide core region and its linkage to the O-specific polysaccharide

Recently it was demonstrated that Shigella dysenteriae type 1, a cause of severe dysentery epidemics, gained its O-specific polysaccharide (O-SP) from Escherichia coli O148. The O-SPs of these bacteria differ only by a galactose residue in the repeat unit of S. dysenteriae type 1 in place of a glucose residue in E. coli O148. Herein, we analyzed the core structure and its linkage to the O-SP in E. coli O148 LPS. Both were found to be identical to those of S. dysenteriae type 1 structures, further supporting the relatedness of these two bacteria. The following structure of the core with one repeat unit of the O-SP has been assigned (all have d-configuration except l-Rha):

Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins

The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.