Carbohydrate Ring Research Articles

Systematic Investigation of Cellular Response to Hydroxyl Group Orientation Differences on Gold Glyconanoparticles.

Nanoparticle (NP) surfaces act as the interface as they interact with living systems and play a critical role in defining their cellular response. The nature of these interactions should be well understood to design safer and more effective NPs to be used in a wide range of biomedical applications. At the moment, it is not clear how a subtle change in surface chemistry will affect an NP's behavior in a biological system. Thus, understanding the role of such a small change is critical and may allow one to fine-tune a biological response. In this study, the cellular response to -OH orientation differences generated on gold glyconanoparticles, which are recently considered promising therapeutic agents as they mimic a glycocalyx, is investigated. As model molecules, glucose and mannose (C2 epimer) as monosaccharides and lactose and maltose (galactose and glucose as free units, C4 epimer) as disaccharides were chosen to monitor the cellular response in A549, BEAS-2b, and MDA-MB-231 cells through cellular uptake, cytotoxicity, and cell cycle progression. The three cell lines gave various and remarkable cellular responses to the same subtle -OH differences on gold glyconanoparticles, and it is determined that not only -OH orientation differences but also the number of saccharides on gold glyconanoparticles affect the cellular response. It was shown that mannose (C2 epimer to glucose) was significant with the promise of being a therapeutic agent for lung cancer therapy, whereas the toxicological profile of MDA-MB-231 cells was affected by AuNPs-glucose the most. This study demonstrates that clearly small chemical alterations on a NP surface can result in a significant cellular response. It can be concluded that the -OH orientation at the second and fourth carbon of a carbohydrate ring has a critical role in designing and engineering novel gold glyconanoparticles (consisting of monolayer mono- or disaccharides) for a specific cancer therapy.

Intramolecular Diels‐Alder Approach to the Construction of Fused Bicyclic 8/6 Ring System of Variecolin

AbstractBicyclo annulations of fused 6/6 and 8/6 ring systems on to a carbohydrate derivative have been achieved. The key step involves an intramolecular Diels‐Alder reaction of a diene and a dienophile tethered through a carbohydrate ring resulting in tricyclic architectures having fused bicycle 6/6 and 8/6 ring systems. The tricyclic structure containing the fused bicyclo 8/6 ring is functionalized for elaboration to the tetracyclic sesterterpene variecolin.

Evaluation of the Thermal and Morphological Properties of γ-Irradiated Chitosan-Glycerol-Based Polymeric Films

Industry-sponsored research has intensified to find suitable substitutes for synthetic polymers. For this purpose, biopolymers are promising materials that are extracted from renewable resources. However, there are areas of concern (biopolymers are mostly brittle in the dry state) that require further research before they are used in advanced applications. To overcome this, plasticizers are often added to biopolymers to enhance their physicochemical properties. In this study, chitosan (CH)-glycerol (GL)-based polymeric films were prepared by a simple drop-casting technique, and the influence of a plasticizer (GL) on the properties of chitosan films was analyzed. Additionally, the as-prepared samples were irradiated with γ-rays (60Co γ rays with a dose of 102 kGy) to study the effect of γ-irradiation on the properties of polymeric composites. To achieve this, different samples were prepared by varying the amount of GL. FT-IR analysis revealed the interruption of hydrogen bonding in chitosan by the incorporation of GL. This led to the chain-spreading of CH, which ultimately increased the flexibility of the composite films (CH-GL). The DSC of the CH film showed two peaks: one endothermic peak below 100 °C (due to water vapor) and a second exothermic peak that appeared between 130 and 360 °C (degradation of the amino group). Plasticization of CH films with GL was confirmed by DSC, where the exothermic degradation was converted into an endothermic peak. Depending upon the amount of GL, γ-irradiation considerably affected the chemical structure of CH by breaking the carbohydrate and pyranose rings; this led to a decrease in the crystallinity of the composite films. The changes studied in the DSC and TGA analysis complemented each other. γ-irradiation also affected the morphology of the films, which changed from smooth and homogeneous to roasted structures, with random swelling on the surface of the films. This swelling reflected the degradation of the surfaces into thin layers. Considering the changes that occurred in the films post-γ-irradiation, it can be inferred that the irradiation dose of 102 kGy is sufficient to degrade as-prepared biopolymer composites.

Recent structural insights into the mechanism of lysozyme hydrolysis.

Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.

Understanding Ring Puckering in Small Molecules and Cyclic Peptides.

The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, 5- and 6-membered carbohydrate rings, and specific macrocycle families. We lack a general understanding of the puckering preferences of medium-sized rings and macrocycles. To address this, we provide an extensive conformational analysis of a diverse set of rings. We used Cremer–Pople puckering coordinates to study the trends of the ring conformation across a set of 140 000 diverse small molecules, including small rings, macrocycles, and cyclic peptides. By standardizing using key atoms, we show that the ring conformations can be classified into relatively few conformational clusters, based on their canonical forms. The number of such canonical clusters increases slowly with ring size. Ring puckering motions, especially pseudo-rotations, are generally restricted and differ between clusters. More importantly, we propose models to map puckering preferences to torsion space, which allows us to understand the inter-related changes in torsion angles during pseudo-rotation and other puckering motions. Beyond ring puckers, our models also explain the change in substituent orientation upon puckering. We also present a novel knowledge-based sampling method using the puckering preferences and coupled substituent motion to generate ring conformations efficiently. In summary, this work provides an improved understanding of general ring puckering preferences, which will in turn accelerate the identification of low-energy ring conformations for applications from polymeric materials to drug binding.

Top-down lignomics analysis of the French pine lignin by atmospheric pressure photoionization quadrupole time-of-flight tandem mass spectrometry: Identification of a novel series of lignin-carbohydrate complexes.

We report the top-down lignomics analysis of the virgin released lignin (VRL) extracted from French pine wood by using atmospheric pressure photoionization quadrupole time-of-flight mass spectrometry (APPI-QqTOF-MS) and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS). We used APPI-QqTOF-MS (positive ion mode) for the analysis of the complex mixture of VRL oligomers extracted from French pine wood. Some of the major precursor ions were fished out from the complex VRL oligomeric mixture and subjected to low-energy CID-MS/MS analyses. Fourteen novel lignin-carbohydrate complexes (LCCs) were identified using APPI-QqTOF-MS/MS of the very complex mixture of virgin released lignins (VRLs), directly extracted from French pine wood without any kind of purification. The low-energy CID-MS/MS analyses allowed us to establish the fragmentation patterns of the precursor ions and to identify the complex structures of the identified LCC molecules. These novel identified series of LCCs were composed of one or two carbohydrate rings to which one, two, or three lignin units were covalently attached. In addition to the fourteen LCCs, acetyl eugenol was identified in the French pine VRL sample. The identification of acetyl eugenol indicates possible lignin degradation and modification (acetylation) during the mild extraction method developed by the Compagnie Industrielle de la Matière Végétale (CIMV). The top-down lignomics analysis of the French pine VRLs using APPI-QqTOF-MS and low energy CID-MS/MS allowed us to identify acetylated eugenol and a novel series of fourteen LCCs. These series of LCCs provide evidence that lignins are covalently linked to carbohydrates in the native wood network and act as cross-linkers between cellulose and hemicellulose components of wood.

Silico-manganese fumes waste encapsulated cryogenic alginate beads for aqueous environment de-colorization

Safe and economical disposal of ultrafine silico-manganese fumes (SMF), a waste, generated during steel production operation is a challenge for environmental chemists. Herein, SMF waste was encapsulated into alginate, lyophilized to form cryogenic SMF beads (cSMFB). The cSMFB was characterized and its adsorptive potential was tested in the removal of methylene blue (MB), methylene green (MG), crystal violet (CV) and celestine blue (CB) from aqueous environment. The cSMFB having respective Brunauer-Emmett-Teller (BET) surface area and Barrett, Joyner, and Halenda (BJH) pore diameter of 59.88 m2/g and 18.58 Å was developed. Fourier transform infra-red (FT-IR) analysis revealed bands at 1630 and 1412 cm−1, attributed to asymmetric and symmetric stretching vibrations of carboxylate ions, characteristic of alginate (used to encapsulate SMF). Also, the bands at 1092 and 1031 cm−1 corresponding to carbohydrate rings of alginate were present. A band ascribed to metal oxides was appeared at 467 cm−1. The encapsulation of SMF waste in alginate was further confirmed by X-ray photoelectron spectroscopy (XPS) (with peaks at binding energies 34, 284.7, and 532 eV ascribed to Na 2p, C1s, and O 1s), X-ray diffraction (XRD) (with 2θ peaks at 13.5 and 22.2° for sodium alginate), and energy-dispersive X-ray (EDX) analyses. The cross-sectional image of pristine cSMFB showed highly porous rough and uneven surface. Thermogravimetric (TGA-DTA) analysis of cSMFB sample revealed the five stages total weight loss of ∼17.5% between 40 and 800 °C. Alkaline pH (pHi range: 6–8) favored the adsorption of dyes, while the equilibration time at Co: 50 mg/L was varied between 480 and 600 min. The adsorption of dyes was possibly governed through electrostatic interaction, coordinate bond formation, and cationic interchange.

Intrinsic dynamic behavior of enzyme:substrate complexes govern the catalytic action of \u03b2-galactosidases across clan GH-A

The conformational itineraries taken by carbohydrate residues in the catalytic subsite of retaining glycoside hydrolases (GHs), harness the link between substrate conformation and reactivity. GHs’ active sites may be described as a combination of subsites dedicated to the binding of individual sugar residues and to catalysis. The three-dimensional structure of GH:carbohydrate complexes has demonstrated that carbohydrate ring conformation changes in an ordered manner during catalysis. Here we demonstrate in silico that a link exists between subsite binding dynamics and substrate specificity for β-galactosidases from clan GH-A families GH1, GH2, GH35, GH42 and GH59. Different oligosaccharides were docked in the active site of reference β-galactosidase structures using Vina-Carb. Subsequent molecular dynamics (MD) simulations revealed that these enzymes favor a high degree of flexibility and ring distortion of the substrate the lytic subsite −1. Although the β-galactosidase families examined are structurally and mechanistically related, distinct patterns of ring distortion were unveiled for the different families. For β-galactosidases, three different family-dependent reaction itineraries (1S3 → 4H3‡ → 4C1, 1,4B → 4H3/ 4E‡ → 4C1, and 1S5 → 4E/ 4H5‡ → 4C1) were identified, all compatible with the antiperiplanar lone pair hypothesis (ALPH) for the hydrolysis of β-glycosides. This comparative study reveals the fuzzy character of the changes in carbohydrate ring geometry prior to carbohydrate hydrolysis.

Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2-Azidofuranoses, 2-Fluorofuranoses and Methyl Furanosyl Uronates.

The 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of SN1 reactions taking place on these reactive intermediates is dictated by the conformation of these species. The nature and configuration of functional groups on the carbohydrate ring affect the stability of glycosyl oxocarbenium ions and control the overall shape of the cations. We herein map the stereoelectronic substituent effects of the C2‐azide, C2‐fluoride and C4‐carboxylic acid ester on the stability and reactivity of the complete suite of diastereoisomeric furanoses by using a combined computational and experimental approach. Surprisingly, all furanosyl donors studied react in a highly stereoselective manner to provide the 1,2‐cis products, except for the reactions in the xylose series. The 1,2‐cis selectivity for the ribo‐, arabino‐ and lyxo‐configured furanosides can be traced back to the lowest‐energy 3 E or E 3 conformers of the intermediate oxocarbenium ions. The lack of selectivity for the xylosyl donors is related to the occurrence of oxocarbenium ions adopting other conformations.

On the molecular factors of sugar beet pulp polyglycans ensuring their water-holding capacity

The basic structural element of the cell walls of beet pulp is dietary fibers, therefore deep processing of this type of raw material is of considerable interest. One of the main physicochemical properties of dietary fibers used in food production is their water holding capacity. However, dietary fibers of beet pulp, as heterogeneous polymer components, are extremely labile to the conditions of their extraction. In this regard, it is relevant to identify technological factors and their rational sequence, in which the target properties will be expressed to the maximum extent. The authors developed an extensive algorithm for the sequential extraction of dietary fibers from beet pulp with selective processing by homofermental preparations, including various options for the preliminary preparation of raw materials. As a result, samples of beet fibers (mainly homogluacutronanes), corresponding to the key graph nodes of the developed algorithm, were identified. For each sample, the magnitude of water holding capacity was determined, as well as the Raman spectrum on an excitation wave of 785 nm with a spectrum scan duration of 3 s and 50 passes per spectrum. In the process of research, the key influence of the degree of saturation of the cell wall matrix with polyvalent metal ions was established. At the same time, in the presence of cations in the matrix, the number of fermentation stages of the same type and their duration play a key role in the formation of water-holding capacity. In the absence of cations, water holding capacity depends only on the nature of the polymer fermentation products. By the method of principal components, it was established that the water-holding capacity is closely related to the activity of oxygen atoms of glycosidic bonds between the links of the polymer chain, as well as the activity of hydroxyl groups not belonging to the carbohydrate ring. However, the main components used describe only 53.5% of the peak heights dispersion, which may indicate participation in the formation of peaks and any third-party factors, which indicates the necessity of further research.

Dynamics of carbohydrate strands in water and interactions with clay minerals: influence of pH, surface chemistry, and electrolytes.

Carbohydrate hydrogels are extensively used in pharmaceuticals and engineered biomaterials. Molecular conformations, assembly, and interactions of the carbohydrate strands with stabilizers such as clay minerals in aqueous solution are difficult to quantify in experiments and the hydrogel properties remain largely a result of trial-and-error studies. We analyzed the assembly of gellan gum in aqueous solution and interactions with dispersed clay minerals in all-atomic detail using molecular dynamics simulation, atomic force microscopy (AFM), and comparisons to earlier measurements. Gellan strands associate at low pH values of 2 and gradually disassemble to double strands with weak association of -0.4 kcal per mole carbohydrate ring as the pH values increases to 9. Ionization of the carbonic acid side groups in the backbone extends the chains and accelerates the conformational dynamics via rapidly changing intramolecular ion bridges. Gellan interactions with clay minerals depend on the strength of electric triple layers between clay, cations, and anionic polymer strands, as well as weaker hydrogen bonds along the edges, which are tunable as a function of the clay surface chemistry, local ionic strength, and pH values. Interaction energies range from -4 to +6 kcal per mol carbohydrate ring and were most favorable for electric triple layers with high charge mobility, which can be achieved for intermediate cation exchange capacity of the clay mineral and high pH values to increase ionization of the clay edges and of the polymer. The findings provide understanding and help control the dynamics and stabilization of carbohydrate hydrogels by clay minerals.

Studies on the molecular dynamics of acetylated oligosaccharides of different topologies (linear versus cyclic)

In this paper, the molecular dynamics and thermal properties of representative acetylated linear and cyclic oligosaccharides: acTRE, acRAF, acSTA, ac-α-CD, ac-β-CD, ac-γ-CD, have been investigated by using broadband dielectric spectroscopy and differential scanning calorimetry. We found that there are marked differences in the dynamics of the structural and secondary relaxation processes in both groups of materials. Just to mention a variation in the distribution of the structural relaxation times as well as different evolutions of the glass transition temperature (Tg) and fragility (m) versus molecular weight (Mw), which seem to be affected by the shape of the molecule, strain in the carbohydrate ring and mobility of side acetyl moieties.

Crystal structure and hydrogen bonding in N-(1-de-oxy-β-d-fructo-pyranos-1-yl)-2-amino-isobutyric acid.

The title compound, alternatively called d-fructose-2-amino-isobutyric acid (FruAib), C10H19NO7, (I), crystallizes exclusively in the β-pyran-ose form, with two conformationally non-equivalent mol-ecules [(IA) and (IB)] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyran-ose, 10.4% β-furan-ose, 10.1% α-furan-ose, 3.0% α-pyran-ose and <0.7% the acyclic forms. The carbohydrate ring in (I) has the normal 2C5 chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyran-ose structures. All carboxyl, hy-droxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intra-molecular hydrogen bonds bridge the amino acid and sugar portions in both mol-ecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar-amino acids suggests an increasing role of intra-molecular heteroatom inter-actions in crystal structures with an increasing proportion of C-H bonds.

Conformational preferences of protonated N-acetylated hexosamines probed by InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy and ab initio calculations

The gas phase IR spectra of three protonated N-acetyl hexosamines and their methyl-blocked α and β anomers are measured in the 3μm spectral range using IRMPD spectroscopy. Using molecular dynamics exploration of the conformational space followed by MP2 energy calculations and DFT simulation of the IR spectra, we propose energetic and spectroscopic arguments to elucidate (i) the site of protonation, (ii) the conformational preference of the carbohydrate ring, and (iii) the contributions of the α and β anomers to the experimental spectra. We report that protonation occurs on the carbonyl group. All isomers of N-acetyl hexosamines are observed in a 4C1 chair conformation regardless of the methylation at the reducing end. Subtle structural variations of this common conformation are described. Finally, anomer-diagnostic spectroscopic features are proposed for GlcNAc and ManNAc.

Multi-scale instrumental analyses for structural changes in steam-treated bamboo using a combination of several solid-state NMR methods

Steam-treated bamboo was analyzed for structural changes at multiple scales using several solid-state NMR methods, including relaxation time analysis. Subtle changes due to different processing conditions were analyzed by 13C magic angle spinning (MAS) NMR using cross polarization (CP), single pulse with dipolar decoupling (DD), and pulse saturation transfer (PST). The analyses also used 1H spin-lattice relaxation time (T1H) integrated with attenuated total reflection infrared spectroscopy (ATR-IR), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). The first change due to the steam treatment appeared in the hemicellulose methyl groups and the aromatic carboxylic acid; with further processing the carbohydrate ring of hemicellulose decreased and the pyrolysis products having quaternary olefinic and aromatic groups increased. During steam treatment, pyrolysis products appear to have restrained molecular motions of the steam-heated bamboo, while cleavage of lignin increased molecular motion of the OCH3 group. Bamboo treated with pressurized steam retained its hemicellulose and produced a smaller amount of pyrolysis products, while both hemicellulose and lignin were reduced by treatment with NaOH solution. The physical fracture of the sample observed at higher processing temperatures and longer times occurred not because of chemical changes in specific constituents but through physical destruction of vascular bundle units.

Crystal structures of three bicyclic carbohydrate derivatives.

The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis-(acet-yloxy)-7-oxo-2-oxabi-cyclo[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acet-yloxy-7-hy-droxy-imino-2-oxobi-cyclo-[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and [(3aR,5R,6R,7R,7aS)-6,7-bis-(acet-yloxy)-2-oxo-octa-hydro-pyrano[3,2-b]pyrrol-5-yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives. They can easily be synthesized in a few steps from commercially available glycals. As a result of the ring strain from the four-membered rings in (I) and (II), the conformations of the carbohydrates deviate strongly from the ideal chair form. Compound (II) occurs in the boat form. In the five-membered lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair conformation. As a result of the distortion of the sugar rings, the configurations of the three bicyclic carbohydrate derivatives could not be determined from their NMR coupling constants. From our three crystal structure determinations, we were able to establish for the first time the absolute configurations of all new stereocenters of the carbohydrate rings.

Enzymatic formation of carbohydrate rings catalyzed by single-walled carbon nanotubes.

Macrocyclic carbohydrate rings were formed via enzymatic reactions around single-walled carbon nanotubes (SWNTs) as a catalyst. Cyclodextrin glucanotransferase, starch substrate and SWNTs were reacted in buffer solution to yield cyclodextrin (CD) rings wrapped around individual SWNTs. Atomic force microscopy showed the resulting complexes to be rings of 12-50 nm in diameter, which were highly soluble and dispersed in aqueous solution. They were further characterized by Raman and Fourier transform infrared spectroscopy and molecular simulation using density functional theory calculation. In the absence of SWNT, hydrogen bonding between glucose units determines the structure of maltose (the precursor of CD) and produces the curvature along the glucose chain. Wrapping SWNT along the short axis was preferred with curvature in the presence of SWNTs and with the hydrophobic interactions between the SWNTs and CD molecules. This synthetic approach may be useful for the functionalization of carbon nanotubes for development of nanostructures.

Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12.

The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the −4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the −2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs.

Mechanism of Adefovir, Tenofovir and Entecavir Resistance: Molecular Modeling Studies of How A Novel Anti-HBV Agent (FMCA) Can Overcome the Drug Resistance

Regardless of significant improvement in the area of anti-HBV therapy, resistance and cross-resistance against available therapeutic agents are the major consideration in drug discovery of new agents. The present study is to obtain the insight of the molecular basis of drug resistance conferred by the B and C domain mutations of HBV-polymerase on the binding affinity of four anti-HBV agents [Adefovir (ADV), Tenofovir (TNF), Entecavir (ETV) & 2'-Fluoro-6'-methylene-carbocyclic adenosine (FMCA)]. In this regard, homology modeled structure of HBV polymerase was used for minimization, conformational search and Glide XP docking followed by binding energy calculation on wild-type as well as on mutant HBV-polymerases (N236T, L180M+M204V+S202G & A194T). Our studies suggest a significant correlation between the fold resistances and the binding affinity of anti-HBV nucleosides. The domain B residue, L180 is indirectly associated with other active-site hydrophobic residues such as A87, F88 and M204, whereas the domain C residue, M204 is closely associated with sugar/pseudosugar ring positioning in the active site. These hydrophobic residues can directly influence the interaction of the incoming nucleoside triphosphates and change the binding efficacy. The carbohydrate ring part of natural substrate dATP, dGTP, FMCA and ETV, are occupied in similar passion in the grooves of HBV polymerase active site. The exocyclic double bond of Entecavir and FMCA occupies in the backside hydrophobic pocket (made by residues A87, F88, L180and M204), which enhances the overall binding affinity. Additional hydrogen bonding interaction of 2'-fluorine of FMCA with R41 residue of polymerase promotes a positive binding in wild-type as well as in ADVr, ETVr and TNFr with respect to that of entecavir.

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains.

This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.