Insights into the Structure of Sucralfate by Advanced Solid- and Liquid-State NMR.

Sucralfate, which is a sucrose octasulfate aluminum complex, is an active pharmaceutical ingredient (API) falling in the category of cytoprotective agents which are very effective for gastric and duodenal ulcers. On interaction with stomach acid, it ionizes into aluminum and sucrose octasulfate ions to form a protective layer over the ulcerated region inhibiting further attack from acid. The mechanism of action of sucralfate in the context of its structure is not well understood. Considering that at least two forms of this API are available in the market, there are no reports on the various forms of sucralfate and differences in their pharmacological action. We characterized the two forms of sucralfate using multinuclear, multidimensional solid-state NMR, and the results show significant structural differences between them arising from variation in the aluminum environment and the level of hydration. The impact of structural differences on pharmacological action was examined by studying acid-induced Al release by 27Al liquid-state NMR. The sucralfate, European pharmaceutical standard, Form I, undergoes faster disruption in acid compared to Form II. The difference is explained on the basis of structural differences in the two forms which gives significant insights into the action of sucralfate in relation to its structure.

On the competition between six-membered and five-membered NHC towards alane centered ring expansion.

The combination of 6-SIDipp·AlH3 (1) and 5-IDipp resulted in the ring expansion of 6-NHC, while the five-membered NHC remained unchanged, which was subsequently explained by DFT studies. Besides, the substitution chemistry of 1 was also studied with TMSOTf and I2, which gave rise to the substitution of a hydride by triflate or iodide ligands.

Unlike RNA-TBA (rTBA), iso-rTBA, the 2'-5'-linked RNA-thrombin-binding aptamer, is a functional equivalent of TBA.

An antiparallel, functional RNA G-quadruplex of the 2'-5'-linked thrombin-binding aptamer (iso-rTBA) is reported for the first time. It can inhibit clotting and is remarkably stable to nuclease-degradation, besides having high thermal stability. It is thus, a superior candidate to TBA, rTBA or isoTBA, for further development as an anticoagulant.

Donor-acceptor based solvent-free organic liquid hybrids with exciplex emission and room temperature phosphorescence.

Solvent-free organic liquids are well-known for their excellent luminescence features. Hence, the recent developments in this area have marked them as potential emitters with high quantum yield and enhanced processability. The support of an available liquid matrix enables doping to deliver hybrid liquids with intriguing luminescence features. In this direction, we report solvent-free liquid donor-acceptor pairs with exciplex emission and room temperature phosphorescence at very low acceptor loading. The underlying weak intermolecular interactions have been revealed by 2D NMR techniques and theoretical calculations. The formation of large-area thin films by exciplex and phosphorescent liquid hybrids will encourage the development of scalable lighting and display materials.

An excimer to exciplex transition through realization of donor-acceptor interactions in luminescent solvent-free liquids.

Luminescent solvent-free organic liquids are known for their enhanced quantum yield, color tunability, and availability of a matrix for other dopants to generate hybrid luminescent materials with improved features for newer applications. Herein, we report a donor-acceptor based luminescent "exciplex liquid" by utilizing the slightly different electron affinity of the acceptor molecules. A red-shifted broad exciplex emission exhibited by the donor-acceptor pair even at a lower concentration of the acceptor (0.001 equiv.) indicates high efficiency in the solvent-free state. A detailed NMR study revealed weak intermolecular interactions between the donor and acceptor in the solvent-free matrix that stabilizes the exciplex liquid. The failure of structurally similar solid counterparts to form an exciplex confirms the advantage of the available supportive liquid matrix. Besides, the luminescent exciplex liquid is found efficient in sensing application, which is unachievable by either the individual liquids or their solid counterparts. Here, a transition of a donor-acceptor pair from a solid to solvent-free liquid results in a new hybrid liquid that can be an alternative for solid sensor materials.

Polymer Nanorings with Uranium Specific Clefts for Selective Recovery of Uranium from Acidic Effluents via Reductive Adsorption.

Nanostructured polymeric materials, functionalized with an appropriate receptor, have opened up newer possibilities for designing a reagent that shows analyte-specific recognition and efficient scavenging of an analyte that has either a detrimental influence on human physiology and environment or on its recovery for further value addition. Higher active surface area, morphological diversity, synthetic tunability for desired surface functionalization, and the ease of regeneration of a nanostructured material for further use have provided such materials with a distinct edge over conventional reagents. The use of a biodegradable polymeric backbone has an added significance owing to the recent concern over the impact of polymers on the environment. Functionalization of biodegradable sodium alginate with AENA (6.85% grafting) as the receptor functionality led to a unique open framework nanoring (NNRG) morphology with a favorable spatial orientation for specific recognition and efficient binding to uranyl ions (U) in an aqueous medium over a varied pH range. Nanoring morphology was confirmed by transmission electron microscopy and atomic force microscopy images. The nanoscale design maximizes the surface area for the molecular scavenger. A combination of all these features along with the reversible binding phenomenon has made NNRG a superior reagent for specific, efficient uptake of UO22+ species from an acidic (pH 3-4) solution and compares better than all existing UO22+-scavengers reported till date. This could be utilized for the recovery of uranyl species from a synthetic acidic effluent of the nuclear power. The results of the U uptake experiments reveal a maximum adsorption capacity of 268 mg of U per g of NNRG in a synthetic nuclear effluent. X-ray photoelectron spectroscopy studies revealed a reductive complexation process and stabilization of U(IV)-species in adsorbed uranium species (U@NNRG).

A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure.

The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alternative splicing, mRNA localization, stabilization, polyadenylation and translation initiation from internal ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5'-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA recognition motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.

Silk Fibroin-Sodium Dodecyl Sulfate Gelation: Molecular, Structural, and Rheological Insights.

A gelling agent is necessary to accelerate sol to gel transition in an aqueous solution of silk fibroin (SF), which otherwise takes several days to complete. In this paper, we investigate the mechanism of gelation of Bombyx mori SF by a model anionic surfactant, sodium dodecyl sulfate (SDS). Even though interactions between SDS and proteins have been extensively investigated, most of these studies have focused on globular proteins, which undergo denaturation. The interaction with a fibrous protein such as SF is different and results in an altered secondary structure leading to gelation. In this work, the concentration-dependent gelation process of the SF-SDS system is examined using rheology, SANS, FTIR, and NMR. We observed preferential binding of SDS to specific regions on the SF chain, which aids structural changes favoring ß-sheet formation. We propose a mechanism for the accelerated sol-gel transition in the SF-SDS system.

Charge transfer liquid: a stable donor-acceptor interaction in the solvent-free liquid state.

Charge-transfer complexes have been an inspiration to develop many functional soft materials. However, most of those studies have focused on solution based assemblies wherein the explicit control of solvents and their polarity are crucial. In this context, we explore an efficient and stable charge transfer liquid using a solvent-free liquid dialkoxynaphthalene donor and a naphthalenediimide acceptor. It has been observed that irrespective of the donor-acceptor ratio, the charge-transfer liquid exhibited an unprecedented stability and retained characteristic features even at increased temperatures. The underlying intermolecular interactions leading to efficient CT have been examined by NMR techniques together with theoretical modelling studies. The concept of charge transfer liquid will be highly beneficial for the development of processable optoelectronically active materials.

Absolute quantitation of poly(R)-3-hydroxybutyric acid using spectrofluorometry in recombinant Escherichia coli.

Poly(R)-3-hydroxybutyric acid (PHB) is a biodegradable natural polymer produced by microorganisms and plants under nitrogen deprivation and physiological stress. Metabolic engineering and synthetic biology approaches are underway to develop strains that can produce PHB and its co-polymers. One of the major limitations to the scaling and success of strain development for biosynthesis of PHB is the absence of fast, accurate, quantitative and scalable methods to estimate PHB in polymer producing cells. In this study, a Nile red-based spectrofluorometric method is developed for absolute quantitation of PHB in recombinant Escherichia coli. The method is a modification of an existing Nile red-based method currently only used for relative quantitation. The two added steps of sonication and ethanol extraction increase the dynamic range of the assay and limit of detection/quantitation. Sonication of PHB standards provides uniform distribution of surface area to volume ratios. This ensures reproducibility and accuracy (lower %relative error) of quantitative staining of granules by Nile red even in a higher dynamic concentration range of 125-1000 µg/ml. Ethanolic extraction of the PHB bound Nile red allows higher recovery and accurate absolute quantitation. To reproduce high recovery and ensure accuracy and precision of the analytical method directly using cells, a protein digestion step was added. This accounted for fluorescence from over-expressed protein and resulted in screening of nonproducers of PHB amongst samples. Thus, the method developed is rapid, accurate, and reproducible, requires low sample volumes and processing compared to other conventional methods. This method is scalable to other PHA's and diverse plastics.

Chiral Discrimination through 1 H†NMR and Luminescence Spectroscopy: Dynamic Processes and Solid Strip for Chiral Recognition.

The appropriate choice of the host molecules with well-defined optical activity (S-H/R-H) helps in the differentiation between two secondary ammonium ion-derivative guest molecules with different optical activities (R-G/S-G) based on the fluorescence resonance energy transfer (FRET)-based luminescence responses. Crown ether-based host molecules with opposite chiral configurations (R-H, S-H) have been derived from 1,1'-bi-2-naphthol (BINOL) derivatives that have axially chiral biaryl centers. These chiral crown ethers form host-guest complexes (i.e., [2]pseudorotaxanes) with chiral secondary ammonium ion derivatives (R-G, S-G). NMR spectroscopic studies show that the complexes are in a dynamic equilibrium in solution. Results of the 1 H NMR and fluorescence spectroscopic studies indicate a head-on orientation of the host and guest in the [2]pseudorotaxanes. The difference in the efficiency in the FRET-based responses between anthracene and the BINOL derivatives allow efficient chiral discrimination of the guests. Isothermal titration calorimetry and NMR investigations reveal that inclusion complexes between hosts and guests of the same chirality (R-H⋅R-G, S-H⋅S-G) are more stable relative to those of opposite chirality (R-H⋅S-G, S-H⋅R-G). However, FRET-based energy-transfer efficiency is higher for R-H⋅S-G and S-H⋅R-G complexes. NMR spectroscopic studies show that the relative orientation of the guest in the host cavity is significantly different when the host binds a guest of the same or opposite chirality; furthermore, the latter is more favorable for FRET, thus enabling discrimination between enantiomers. Interestingly, chiral discrimination of guest ions could also be achieved by using silica surfaces modified with chiral host molecules.

Cucurbit[7]uril Induced Formation of FRET-Enabled Unilamellar Lipid Vesicles.

A unique fluorescence resonance energy transfer (FRET) process is found to be operational in a unilamellar lipid self-assembly in the aqueous phase. A newly synthesized naphthyl based long chain lipid derivative [N-(naphthalene-1-ylmethyl)tetradecane-1-ammonium chloride, 14NA+] forms various self-assembled architectures in the aqueous phase. Controlled changes in lipid concentration lead to a transition of the self-assemblies from micelles to vesicles to rods. In the presence of cucurbit[7]uril (CB7), 14NA+ forms a host-guest [2]pseudorotaxane complex (CB7∋14NA+) and secondary interactions lead to the formation of a lipid bilayer with hydrophobic pockets situated in between the layers. The change in the structure of 14NA+ assemblies, interaction with CB7 and formation of supramolecular assemblies of CB7∋14NA+ were examined using light scattering, spectroscopic, and microscopic techniques. Entrapment of a luminescent dye, anthracene within the hydrophobic bilayer of the supramolecular assembly CB7∋14NA+ favors a modified luminescent response due to an efficient FRET process. Further, the FRET process could be controlled by thermal and chemical stimuli that induce transformation of unilamellar vesicles.

Silk Fibroin-Sophorolipid Gelation: Deciphering the Underlying Mechanism.

Silk fibroin (SF) protein, produced by silkworm Bombyx mori, is a promising biomaterial, while sophorolipid (SL) is an amphiphilic functional biosurfactant synthesized by nonpathogenic yeast Candida bombicola. SL is a mixture of two forms, acidic (ASL) and lactonic (LSL), which when added to SF results in accelerated gelation of silk fibroin. LSL is known to have multiple biological functionalities and hence hydrogels of these green molecules have promising applications in the biomedical sector. In this work, SANS, NMR, and rheology are employed to examine the assembling properties of individual and mixed SLs and their interactions with SF to understand the mechanism that leads to rapid gelation. SANS and NMR studies show that ASL assembles to form charged micelles, while LSL forms micellar assemblies and aggregates of a mass fractal nature. ASL and LSL together form larger mixed micelles, all of which interact differently with SF. It is shown that preferential binding of LSL to SF causes rapid unfolding of the SF chain leading to the formation of intermolecular beta sheets, which trigger fast gelation. Based on the observations, a mechanism for gelation of SF in the presence of different sophorolipids is proposed.

Tuning Emission Responses of a Triphenylamine Derivative in Host-Guest Complexes and an Unusual Dynamic Inclusion Phenomenon.

A newly synthesized triphenylamine derivative (1Cl3) shows significant differences in inclusion complex formation with two different macrocyclic hosts, cucurbit[7]uril (CB[7]) and ß-cyclodextrin (ß-CD). Detailed investigations by NMR spectroscopy reveal that CB[7] forms a 1:3 host-guest complex ([1·3{CB[7]}]Cl3) in which three arms of 1Cl3 are bound to three host molecules. On the other hand, ß-CD forms a dynamic 1:1 inclusion complex ([1·{ß-CD}]Cl3) by binding to only one of the three arms of 1Cl3 at a given time. The formation of a 1:1 host-guest complex with ß-CD and 1:3 host-guest complex with CB[7] was also confirmed from the results of the isothermal titration calorimetric studies. Interestingly, 1Cl3 exhibits a rare dual emission property in solution at room temperature with the lower and higher energy bands arising from a locally excited state and an intramolecular charge-transfer transition, respectively. The difference in inclusion complex formation behavior of 1Cl3 with the two macrocyclic hosts results in the stabilization of different emission states in the two inclusion complexes. The fundamental difference in the electrostatic surface potentials, cavity polarities, and shapes of the two macrocyclic hosts could account for the formation of the different inclusion complexes with distinct luminescence responses.

Increase in backbone mobility of the VTS1p-SAM domain on binding to SRE-RNA.

The sterile alpha motif (SAM) domain of VTS1p, a posttranscriptional gene regulator, belongs to a family of SAM domains conserved from yeast to humans. Even though SAM domains were originally classified as protein-protein interaction domains, recently, it was shown that the yeast VTS1p-SAM and the SAM domain of its Drosophila homolog Smaug can specifically recognize RNA hairpins termed Smaug recognition element (SRE). Structural studies of the SRE-RNA complex of VTS1p-SAM revealed that the SAM domain primarily recognizes the shape of the RNA fold induced by the Watson-Crick base-pairing in the RNA pentaloop. Only the central G nucleotide is specifically recognized. The VTS1p-SAM domain recognizes SRE-RNAs with a CNGGN pentaloop where N is any nucleotide. The C1-G4 base pair in the wild type can be replaced by any pair of nucleotides that can form base pairs even though the binding affinity is greatest with a pyrimidine in position 1 and a purine in position 4. The interaction thus combines elements of sequence-specific and non-sequence-specific recognitions. The lack of structural rearrangements in either partner following binding is rather intriguing, suggesting that molecular dynamics may play an important role in imparting relaxed specificity with respect to the exact combination of nucleotides in the loop, except for the central nucleotide. In this work, we extend our previous studies of SRE-RNA interaction with VTS1p, by comparing the dynamics of the VTS1p-SAM domain both in its free form and when bound to SRE-RNA. The 15N relaxation studies of backbone dynamics suggest the presence of a dynamic interaction interface, with residues associated with specific G3 recognition becoming more rigid on RNA binding while other regions attain increased flexibility. The results parallel the observations from our studies of dynamics changes in SRE-RNA upon binding to VTS1p-SAM and shows that molecular dynamics could play a crucial role in modulating binding affinity and possibly contribute to the free energy of the interaction through an entropy-driven mechanism.

Changes in dynamics of SRE-RNA on binding to the VTS1p-SAM domain studied by 13C NMR relaxation.

RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative (13)C NMR relaxation study of the changes in RNA dynamics in the pico-nanosecond time scale and micro-millisecond time scale resulting from interaction of the stem-loop SRE-RNA with the VTS1p-SAM domain. (13)C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully (13)C/(15)N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.

Sheet-forming abiotic hetero foldamers.

Abiotic hetero oligomers, adopting a well-defined extended self-assembled sheet-like structure, derived from conformationally constrained aliphatic and aromatic amino acid residues repeating at regular intervals are reported.

Conformationally constrained aliphatic-aromatic amino-acid-conjugated hybrid foldamers with periodic beta-turn motifs.

In this note, we describe the design, synthesis, and structural studies of novel hybrid foldamers derived from Aib-Pro-Adb building blocks that display repeat beta-turn structure motif. The foldamer having a conformationally constrained aliphatic-aromatic amino acid conjugate adopts a well-defined, compact, three-dimensional structure, governed by a combined conformational restriction imposed by the individual amino acids with which it is made of. Conformational investigations by single-crystal X-ray and solution-state NMR studies were undertaken to investigate the conformational preference of these foldamers with a hetero-backbone. Our findings suggest that constrained aliphatic-aromatic amino acid conjugates would offer new avenues for the de novo design of hybrid foldamers with distinctive structural architectures.