Chemo-enzymatic synthesis of conformationally constrained oligosaccharides

N-Acetyllactosamine derivative 4, which has a methylene amide tether between C-6 and C-2', was enzymatically glycosylated using rat liver alpha-2,6-sialyltransferase (ST6GalI) or recombinant human fucosyltransferase V (FucT-V) to give conformationally constrained trisaccharides 5 and 6, respectively. The methylene amide linker of 4 was installed by a two-step procedure, which involved acylation of a C-6 amino function of a LacNAc derivative with chloroacetic anhydride followed by macrocyclization by nucleophilic displacement of the chloride by a C-2' hydroxyl. The conformational properties of 4 were determined by a combination of NOE and trans-glycosidic heteronuclear coupling constant measurements and molecular mechanics simulations and these studies established that the glycosidic linkage of 4 is conformationally constrained and resides in only one of the several energy minima accessible to LacNAc. The apparent kinetic parameters of transfer to LacNAc and conformationally constrained saccharides 3 and 4 indicates that fucosyltransferase V recognize LacNAc in its A-conformer whereas alpha-2,6-sialyltransferase recognizes the B-conformer of LacNAc.     

Optimised N-acetyl-d-lactosamine synthesis using Thermus thermophilus β-galactosidase in bio-solvents

Synthesis of N-acetyl-d-lactosamine (Gal-β[1→4]GlcNAc, LacNAc) catalyzed by β-galactosidase from Thermus thermophilus (TTP0042) is affected by side reactions that give as result very low yields (about 20%) of LAcNAc when the reaction is performed in buffer. The process is improved (up to 91% of disaccharide yield) when the reaction takes place in the presence of solvents from biomass (bio-solvents) at 2.0 M concentration. Most of the solvents tested increased the LacNAc synthesis and reduced the undesired side reactions. In order to understand the possible effects of these solvents over the enzyme regioselectivity, we developed a conformational study of the enzyme structure in the presence of a selected bio-solvent by circular dichroism and fluorescence. According to this study, we were able to conclude that the presence of bio-solvents in the reaction media modifies the enzyme secondary and tertiary structure and this may be the cause of the regioselectivity changes observed in the transglycosylation reaction.     

Protein flexibility as revealed by fluorescence resonance energy transfer: an extension of the method for systems with multiple labels

The temperature profile of the normalized fluorescence resonance energy transfer efficiency is capable of monitoring the relative change of flexibility and/or conformational state of macromolecules [Biochemistry 23 (1984) 3403]. The method described earlier for one donor-one acceptor systems is extended to multiple fluorophore systems when the energy transfer occurs between either one donor-m acceptors, or n donors-one acceptor or n donors-m acceptors (where n and m are integer values). It is shown that the normalized energy transfer efficiency obtained for systems containing multiple labels is a linear combination of the normalized transfer efficiency assigned to individual donor-acceptor pairs of the system, thus its temperature profile is capable of monitoring the change of intramolecular flexibility and/or conformational state.     

Force field parametrization and molecular dynamics simulation of flexible POSS-linked (NHC; phosphine) Ru catalytic complexes

In recent years, N-heterocyclic carbene (NHC) or phospine groups have been put forward as candidate catalysts ligands for olefin metathesis reactions to be performed using multistep methods. Some of these proposed ligands contain polyhedral oligomeric silsesquioxane (POSS) structures linked to NHC rings by means of alkyl chains. Some important properties for the prediction of catalytic activity, such as the theoretically defined buried volume, are related to the conformational characteristics of these complex ligands that can be studied through molecular dynamics simulations. However, the chemical structure of resulting catalytic complexes usually contains atoms or groups that are not included in the common forcefields used in simulations. In this work we focus on complexes formed by a catalytic metal center (Ru) with both phospine and POSS-linked NHC groups. The central part of the complexes contain atoms and groups that have bonds, bond angles, and torsional angles whose parameters have not been previously evaluated and included in existing force fields. We have performed basic ab initio quantum mechanical calculations based on the density functional theory to obtain energies for this central section. The force field parameters for bonds, bond angles, and torsional angles are then calculated from an analysis of energies calculated for the equilibrium and different locally deformed structures. Nonbonded interactions are also conveniently evaluated. From subsequent molecular dynamics simulations, we have obtained results that illustrate the conformational characteristics most closely connected with the catalytic activity.     

Macrocyclic Encapsulation in a Non-fused Tetrathiophene Acceptor for Efficient Organic Solar Cells with High Short-Circuit Current Density

Non-fullerene acceptors have shown great promise for organic solar cells (OSCs). However, challenges in achieving high efficiency molecular system with conformational unicity and effective molecular stacking remain. In this study, we present a new design of non-fused tetrathiophene acceptor R4T-1 via employing the encapsulation of tetrathiophene with macrocyclic ring. The single crystal structure analysis reveals that cyclic alkyl side chains can perfectly encapsulate the central part of molecule and generate a conformational stable and planar molecular backbone. Whereas, the control 4T-5 without the encapsulation restriction displays cis- and twisted conformation. As a result, R4T-1 based OSCs achieved an outstanding power conversion efficiency (PCE) exceeding 15.10 % with a high short-circuit current density (J_sc) of 25.48 mA/cm², which is significantly improved by ≈30 % in relative to that of the control. Our findings demonstrate that the macrocyclic encapsulation strategy could assist fully non-fused electron acceptors (FNEAs) to achieve a high photovoltaic performance and pave a new way for FNEAs design.     

Catalytic addition of metallo-aldehyde enolates to ketones: a new C-C bond-forming hydrogenation

The first catalytic cross-aldolization of metallo-aldehyde enolates with ketone acceptors is enabled via hydrogenation of keto-enals with cationic rhodium catalysts. These results, in conjunction with prior studies involving the catalytic hydrogen-mediated reductive coupling of enones, dienes, and diynes with carbonyl acceptors, support the feasibility of developing a broad new class of catalytic C-C bond formations based on the electrophilic trapping of hydrogenation intermediates. [reaction: see text]     

The first conjugate addition reaction of terminal alkynes catalytic in copper: conjugate addition of alkynes in water

We document that alkynyl copper reagents generated under aqueous conditions from terminal acetylenes, catalytic Cu(OAc)2, and sodium ascorbate undergo additions to Meldrum's acid-derived Michael acceptors at room temperature (Scheme 1). The additions are not only novel, but also constitute the first example of the conjugate addition reaction of an acetylide catalytic in copper.     

Structural and thermodynamic studies on cation-Pi interactions in lectin-ligand complexes: high-affinity galectin-3 inhibitors through fine-tuning of an arginine-arene interaction

The high-resolution X-ray crystal structures of the carbohydrate recognition domain of human galectin-3 were solved in complex with N-acetyllactosamine (LacNAc) and the high-affinity inhibitor, methyl 2-acetamido-2-deoxy-4-O-(3-deoxy-3-[4-methoxy-2,3,5,6-tetrafluorobenzamido]-beta-D-galactopyranose)-beta-D-glucopyranoside, to gain insight into the basis for the affinity-enhancing effect of the 4-methoxy-2,3,5,6-tetrafluorobenzamido moiety. The structures show that the side chain of Arg144 stacks against the aromatic moiety of the inhibitor, an interaction made possible by a reorientation of the side chain relative to that seen in the LacNAc complex. Based on these structures, synthesis of second generation LacNAc derivatives carrying aromatic amides at 3'-C, followed by screening with a novel fluorescence polarization assay, has led to the identification of inhibitors with further enhanced affinity for galectin-3 (K(d) > or = 320 nM). The thermodynamic parameters describing the binding of the galectin-3 C-terminal to selected inhibitors were determined by isothermal titration calorimetry and showed that the affinity enhancements were due to favorable enthalpic contributions. These enhancements could be rationalized by the combined effects of the inhibitor aromatic structure on a cation-Pi interaction and of direct interactions between the aromatic substituents and the protein. The results demonstrate that protein-ligand interactions can be significantly enhanced by the fine-tuning of arginine-arene interactions.     

Chemical consequences of conformation in macrocyclic compounds : An effective approach to remote asymmetric induction

In this paper we show that the conformational properties of medium- and large-ring organic molecules have profound consequences on the stereochemical course of their chemical reactions. Kinetic enolate alkylations, dimethylcuprate additions and catalytic hydrogenations were examined on a variety of monosubstituted 8- to 12-membered macrocyclic ketones and lactones, and the diastereomeric composition of the products was determined. In many systems a single Me substituent provided enough conformational bias to allow highly stereoselective formation of new asymmetric centers. The diastereoselection exhibited by the reactions investigated appears to be intimately associated with the conformational properties of the macrocyclic substrates employed since simple molecular mechanics calculations allowed semiquantitative prediction of the product distributions in every case.     

When does the Michaelis-Menten equation hold for fluctuating enzymes?

Enzymes are dynamic entities: both their conformation and catalytic activity fluctuate over time. When such fluctuations are relatively fast, it is not surprising that the classical Michaelis-Menten (MM) relationship between the steady-state enzymatic velocity and the substrate concentration still holds. However, recent single-molecule experiments have shown that this is the case even for an enzyme whose catalytic activity fluctuates on the 10(-4)-10 s range. The purpose of this paper is to examine various scenarios in which slowly fluctuating enzymes would still obey the MM relationship. Specifically, we consider (1) the quasi-static condition (e.g., the conformational fluctuation of the enzyme-substrate complex is much slower than binding, catalysis, and the conformational fluctuations of the free enzyme), (2) the quasi-equilibrium condition (when the substrate dissociation is much faster than catalysis, irrespective of the time scales or amplitudes of conformational fluctuations), and (3) the conformational-equilibrium condition (when the dissociation and catalytic rates depend on the conformational coordinate in the same way). For each of these scenarios, the physical meaning of the apparent Michaelis constant and catalytic rate constant is provided. Finally, as an example, the theoretical analysis of a recent single-molecule enzyme assay is considered in light of the perspectives presented in this paper.     

Galectin–Glycan Interactions: Guidelines for Monitoring by 77Se NMR Spectroscopy,and Solvent (H2O/D2O) Impact on Binding

Functional pairing between cellular glycoconjugates and tissue lectins like galectins has wide (patho)physiological significance. Their study is facilitated by nonhydrolysable derivatives of the natural O-glycans, such as S- and Se-glycosides. The latter enable extensive analyses by specific ⁷⁷Se NMR spectroscopy, but still remain underexplored. By using the example of selenodigalactoside (SeDG) and the human galectin-1 and -3, we have evaluated diverse ⁷⁷Se NMR detection methods and propose selective ¹H,⁷⁷Se heteronuclear Hartmann–Hahn transfer for efficient use in competitive NMR screening against a selenoglycoside spy ligand. By fluorescence anisotropy, circular dichroism, and isothermal titration calorimetry (ITC), we show that the affinity and thermodynamics of SeDG binding by galectins are similar to thiodigalactoside (TDG) and N-acetyllactosamine (LacNAc), confirming that Se substitution has no major impact. ITC data in D₂O versus H₂O are similar for TDG and LacNAc binding by both galectins, but a solvent effect, indicating solvent rearrangement at the binding site, is hinted at for SeDG and clearly observed for LacNAc dimers with extended chain length.     

Electron donating properties and catalytic activity of samarium oxide and its mixed oxides with alumina

The catalytic activity of Sm₂O₃ and its mixed oxides with alumina in the Oppenauer oxidation of a secondary alcohol and Meerwein-Ponndorf-Verley reduction of ketones is reported. The data were correlated with their surface electron donor properties. The electron donating properties of the oxides have been determined from the adsorption of electron acceptors of various electron affinity on the surface of these oxides.     

Characterization of lipooligosaccharides from Haemophilus ducreyi containing polylactosamine repeats

Haemophilus ducreyi, a gram-negative human mucosal pathogen, is one of the principal causes of genital ulcer disease. The lipooligosaccharides (LOS) of these bacteria are considered to be a major virulence factor and have been implicated in the adherence and invasion of H. ducreyi to several human cell types. An isogenic heptosyltransferase-III knockout strain (waaQ) was recently constructed from H. ducreyi 35000 wild-type strain and immunochemical and molecular weight data of the isolated LOS suggested the presence of poly-N-acetyllactosamine (LacNAc) (Filiatrault et al., Infect. Immun. 2000, 68, 3352-3361). In this present study, the structures of these novel LOS-glycoforms were characterized by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry in combination with exoglycosidase digestion. Detailed structural information was obtained for the oligosaccharide (OS) portions of these LOS showing between one to five linear LacNAc repeats on the non-reducing terminus of the main oligosaccharide branch. When grown on solid media, the organism produced LacNAc repeats that were further modified by the addition of sialic acid. Enzymatic digestion with beta-galactosidase, beta-N-acetylhexosaminidase, and neuraminidase type VI-A yielded truncated glycoforms consistent with a polyLacNAc structure capped at various end points with sialic acid. ESI-MS/MS mass spectrometry on a quadrupole time-of-flight instrument was particularly effective in obtaining detailed structural information on the least abundant, high-mass glycoforms. Although LOS containing terminal di-LacNAc have been reported, this is the first time to our knowledge that a linear polyLacNAc structure has been characterized in bacteria.     

Thioglycosynthases: double mutant glycosidases that serve as scaffolds for thioglycoside synthesis

A double mutant, retaining glycosidase that lacks both the catalytic nucleophile and the catalytic acid/base residues efficiently catalyzes thioglycoside formation from a glycosyl fluoride donor and thiosugar acceptors.     

Two-Step covalent immobilization of enzymes as a way for study of effects influencing catalytic activity

Isothiocyanatopropyl derivatives of trypsin and pepsin obtained by treatment with 3isothiocyanato-1-propyl isocyanate (in the first step) can be covalently bound to carriers having amino groups. Besides all the general principles valid for reactions of isothiocyanates with amines, prerequisite for the satisfactory coupling properties of isothiocyanatopropyl derivatives are (a) a sufficiently high modification degree with isothiocyanate, and (b) a concentration excess of NH₂ carrier groups. With respect to the coupling properties, nonspecific sorptions and the catalytic properties of the immobilized trypsin isothiocyanatopropy l derivatives, the better carrier appears to be the cross-linked polyethy leneimine. Isothiocyanatopropyl, 3-isothiocyanato-bromopropyl, and isothiocyanatopenty l derivatives of leucine, insulin, and albumin also have good coupling properties. The mode in which the amidolytic and caseinolytic activity of isothiocyanatopropyl derivatives of trypsin was influenced after its immobilization on polyethyleneimine clearly indicated that the functional groups of the enzyme did not participate in the coupling to the carrier. Moreover, no intermolecular reactions were observed during the immobilization process. On the other hand, the conformational changes of the protein molecule are important, since they probably influence the changes in the catalytic properties of modified enzymes after their immobilization.     

The role of carbonyl and thiocarbonyl groups in the conformational isomerism of haloacetones and halothioacetones

The presumable, but not well-known parallelism between carbonyl and thiocarbonyl groups as electron acceptors in conformational analysis is reported. Our theoretical investigation was carried out for model compounds, namely mono-haloacetones and mono-halothioacetones. Furthermore, the donor ability of C–H and C–halo bonds has been evaluated on the basis of natural bond orbital (NBO) analysis and orbital levels calculations, and the conformational isomerism discussed in terms of classical and hyperconjugative interactions. It has been found that the conformational behavior of the titled compounds is strongly dependent on the π donor/acceptor behavior, which differs substantially between C=O and C=S systems, as well as on the steric/electrostatic and non-Lewis-type interactions involving the series of halogens.     

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically tuned to exchange on the millisecond time scale. The conformational changes of the protein backbone during catalysis were followed by (15)N nuclear spin relaxation dispersion experiments. A conformational transition that is well described by a two-state process with an exchange rate corresponding to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions on the time scale of catalytic turnover were not observed for the enzyme in the resting states, implying that alternative conformers do not accumulate to significant concentrations. These results infer that the turnover rate in glutaredoxin is governed by formation of a productive enzyme-substrate encounter complex, and that catalysis proceeds by an induced fit mechanism rather than by conformer selection driven by intrinsic conformational dynamics.     

Harnessing the Structure-Performance Relationships in Designing Non-Fused Ring Acceptors for Organic Solar Cells

The prerequisite for commercially viable organic solar cells (OSC) is to reduce the efficiency-stability-cost gap. Therefore, the cost of organic materials should be reduced by minimizing the synthetic steps, yet maintaining the molecular planarity and efficiencies achieved by the fused ring acceptors (FRA). In this respect, developing non-fused ring acceptors (NFRA) with suitable functionalization to favor conformational planarity and effective molecular packing is beneficial and cost-effective. Presently, the power conversion efficiency (PCE) for NFRAs is around 16 %, yet lower than the 19 % achieved for FRAs. Despite their potential, a thorough understanding of the effective structural design of NFRAs is necessary for developing efficient OSCs. This article pays special attention to the molecular design concept for NFRAs developed in the last years and analyzed the approach toward materials design and efficiency improvement, an important step toward technological application.