Numerical simulation of peristalsis to study co-localization and intestinal distribution of a macromolecular drug and permeation enhancer.

In this work, simulations of intestinal peristalsis are performed to investigate the intraluminal transport of macromolecules (MMs) and permeation enhancers (PEs). Properties of insulin and sodium caprate (C10) are used to represent the general class of MM and PE molecules. Nuclear magnetic resonance spectroscopy was used to obtain the diffusivity of C10, and coarse-grain molecular dynamics simulations were carried out to estimate the concentration-dependent diffusivity of C10. A segment of the small intestine with the length of 29.75 cm was modeled. Peristaltic speed, pocket size, release location, and occlusion ratio of the peristaltic wave were varied to study the effect on drug transport. It was observed that the maximum concentration at the epithelial surface for the PE and the MM increased by 397 % and 380 %, respectively, when the peristaltic wave speed was decreased from 1.5 to 0.5 cm s-1. At this wave speed, physiologically relevant concentrations of PE were found at the epithelial surface. However, when the occlusion ratio is increased from 0.3 to 0.7, the concentration approaches zero. These results suggest that a slower-moving and more contracted peristaltic wave leads to higher efficiency in transporting mass to the epithelial wall during the peristalsis phases of the migrating motor complex.

Antiviral iridoid glycosides from Clerodendrum myricoides.

The methanol root extract of Clerodendrum myricoides (Hochst.) Vatke afforded two new (1, 2) and two known (3, 4) iridoid glycosides. The structures of the isolated compounds were established based on NMR, IR, UV and MS data analyses. The crude extract and the isolated constituents were assayed for antiviral activity against the human respiratory syncytial virus (RSV) in human laryngeal epidermoid carcinoma (HEp-2) cells. The crude extract inhibited RSV infectivity at EC50 = 0.21 µg/ml, while it showed cytotoxicity against HEp-2 cells with CC50 = 9 µg/ml. Compound 2 showed 43.2% virus inhibition at 100 µM, while compounds 1 as well as 3 and 4 had only weak antiviral and cytotoxic activities.

Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family.

The first S-adenosyl methionine (SAM) degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as a SAM hydrolase forming 5'-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography, and nuclear magnetic resonance spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis and in vitro and in vivo mutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.

Bacteria can be infected by viruses known as bacteriophages. These viruses inject their genetic material into bacterial cells and use the bacteria's own machinery to build the proteins they need to survive and infect other cells. To protect themselves, bacteria produce a molecule called S-adenosyl methionine, or SAM for short, which deposits marks on the bacteria's DNA. These marks help the bacteria distinguish their own genetic material from the genetic material of foreign invaders: any DNA not bearing the mark from SAM will be immediately broken down by the bacterial cell. This system helps to block many types of bacteriophage infections, but not all. Some bacteriophages carry genes that code for enzymes called SAMases, which can break down SAM, switching off the bacteria's defenses. The most well-known SAMase was first discovered in the 1960s in a bacteriophage called T3. Chemical studies of this SAMase suggested that it works as a 'hydrolase', meaning that it uses water to break SAM apart. New SAMases have since been discovered in bacteriophages from environmental water samples, which, despite being able to degrade SAM, are genetically dissimilar to one another and the SAMase in T3. This brings into question whether these enzymes all use the same mechanism to break SAM down. To gain a better understanding of how these SAMases work, Guo, Söderholm, Kanchugal, Isaksen et al. solved the crystal structure of one of the newly discovered enzymes called Svi3-3. This revealed three copies of the Svi3-3 enzyme join together to form a unit that SAM binds to at the border between two of the enzymes. Computer simulations of this structure suggested that Svi3-3 holds SAM in a position where it cannot interact with water, and that once in the grip of the SAMase, SAM instead reacts with itself and splits into two. Experiments confirmed these predictions for Svi3-3 and the other tested SAMases. Furthermore, the SAMase from bacteriophage T3 was also found to degrade SAM using the same mechanism. This shows that this group of SAMases are not hydrolases as originally thought, but in fact 'lyases': enzymes that break molecules apart without using water. These findings form a starting point for further investigations into how SAM lyases help bacteriophages evade detection. SAM has various different functions in other living organisms, and these lyases could be used to modulate the levels of SAM in future studies investigating its role.

Antibacterial and cytotoxic prenylated dihydrochalcones from Eriosema montanum.

Two new prenylated dihydrochalcones (1,2) and eighteen known secondary metabolites (3-20) were isolated from the CH2Cl2-MeOH (1:1) extracts of the roots, the stem bark and the leaves of Eriosema montanum Baker f. (Leguminosae). The structures of the isolated compounds were characterized by NMR, IR, and UV spectroscopic and mass spectrometric analyses. The structures of compounds 5, 10, 11 and 13 were confirmed by single crystal X-ray diffraction. The antibacterial activity of the crude extracts and the isolated constituents were established against Gram-positive and Gram-negative bacteria. Among the tested compounds, 1-4 and 10 showed strong activity against the Gram-positive bacterium Bacillus subtilis with minimum inhibitory concentration (MIC) ranging from 3.1 to 8.9 µM, as did the leaf crude extract with an MIC of 3.0 µg/mL. None of the crude extracts nor the isolated compounds were active against Escherichia coli. Compounds 1, 3 and 4 showed higher cytotoxicity, evaluated against the human breast cancer cell line MCF-7, with EC50 of 7.0, 18.0 and 18.0 µM, respectively. These findings contribute to the phytochemical understanding of the genus Eriosema, and highlight the pharmaceutical potential of prenylated dihydrochalcones.

In Vitro Performance and Chemical Stability of Lipid-Based Formulations Encapsulated in a Mesoporous Magnesium Carbonate Carrier.

Lipid-based formulations can circumvent the low aqueous solubility of problematic drug compounds and increase their oral absorption. As these formulations are often physically unstable and costly to manufacture, solidification has been suggested as a way to minimize these issues. This study evaluated the physicochemical stability and in vitro performance of lipid-loaded mesoporous magnesium carbonate (MMC) particles with an average pore size of 20 nm. A medium chain lipid was loaded onto the MMC carrier via physical adsorption. A modified in vitro lipolysis setup was then used to study lipid release and digestion with 1H nuclear magnetic resonance spectroscopy. The lipid loading efficiency with different solidification techniques was also evaluated. The MMC, unlike more commonly used porous silicate carriers, dissolved during the lipolysis assay, providing a rapid release of encapsulated lipids into solution. The digestion of the dispersed lipid-loaded MMC therefore resembled that of a coarse dispersion of the lipid. The stability data demonstrated minor degradation of the lipid within the pores of the MMC particles, but storage for three months did not reveal extensive degradation. To conclude, lipids can be adsorbed onto MMC, creating a solid powder from which the lipid is readily released into the solution during in vitro digestion. The chemical stability of the formulation does however merit further attention.

Effect of ring rize on photoisomerization properties of stiff stilbene macrocycles.

A series of stiff stilbene macrocycles have been studied to investigate the possible impact of the macrocycle ring size on their photodynamic properties. The results show that reducing the ring size counteracts the photoisomerization ability of the macrocycles. However, even the smallest macrocycle studied (stiff stilbene subunits linked by a six carbon chain) showed some degree of isomerization when irradiated. DFT calculations of the energy differences between the E- and Z-isomers show the same trend as the experimental results. Interestingly the DFT study highlights that the energy difference between the E- and Z-isomers of even the largest macrocycle (linked by a twelve carbon chain) is significantly higher than that of the stiff stilbene unit itself. In general, it is indicated that addition of even a flexible chain to the stiff stilbene unit may significantly affect its photochemical properties and increase the photostability of the resulting macrocycle.

Formation of persistent organic diradicals from N,N'-diphenyl-3,7-diazacyclooctanes.

ABSTRACT: N,N'-Diphenyl-3,7-diazacyclooctane and structurally related N,N'-diphenylbispidine derivatives react with silver(I) ions in a high-yielding C-C coupling reaction to produce dication-diradical species, with the silver ions serving a double function both as template and as an oxidant. The resulting bis(benzidino)phane derivatives are persistent organic radicals, stable for several months in solution as well as in the solid state, at room temperature and above, as well as being exposed to the atmosphere. The molecular structure features a double-decker cyclophane motif, stabilized by intramolecular π-dimerization of two delocalized benzidinium radical segments. Intermolecular π-dimers are formed in the solid state.

Design of oxophilic metalloporphyrins: an experimental and DFT study of methanol binding.

By systematic measurements we have evaluated a series of tetraphenyl metalloporphyrins and halogenated tetraphenyl metalloporphyrin derivatives for binding to ligands with oxygen containing functional groups, using methanol, acetic acid and acetone as examples. Experimental binding constants identified three metalloporphyrins with good binding to all three ligands: MgTPFPP, MgTPPBr8 and ZnTPPBr8 as well as a range of porphyrins binding to select ligands. Based on these results the optimal porphyrins can be selected for the desired binding interactions. We also show how to use DFT calculations to evaluate the potential binding between a metalloporphyrin and a ligand, which is deduced from free energies of binding ΔG, charge transfer ΔQ, and change of metal spin state. Computations on unsubstituted porphyrins in lieu of tetraphenyl porphyrin systems yield reliable predictions of binding interactions with good correlation to the corresponding experimental data. The calculations have also yielded interesting insights into the effect of halogenation in the ß-position on the binding to ligands with oxygen containing functional groups.

Exciton-Coupled Circular Dichroism Characterization of Monotopically Binding Guests in Host-Guest Complexes with a Bis(zinc porphyrin) Tweezer.

A stiff-stilbene-linked bisporphyrin tweezer with inherent helicity was used for exciton-coupled circular dichroism (ECCD) characterization of a series of monotopically binding amine guest molecules. CD signals were observed for a variety of monoamines at relatively low tweezer/amine (host/guest) ratios between 1 : 10 to 1 : 70. For the amines producing the most intense CD signals, a binding stoichiometry of 1 : 2 was found. A likely explanation is the presence of guest-guest interactions in the complexes. This is supported by the correlation observed between CD signal intensity and magnitude of possible noncovalent binding between the guests, which can be divided into three groups showing no, moderate and strong response, respectively. Further support for this rationalization comes from molecular modelling.

Conducting redox polymers with non-activated charge transport properties.

Non-activated charge transport has been demonstrated in terephthalate-functionalized conducting redox polymers. The transition from a temperature-activated conduction mechanism to a residual scattering mechanism was dependent on the doping level. The latter mechanism is associated with apparent negative activation barriers to charge transport and is generally found in polymer materials with a high degree of order. Crystallographic data, however, suggested a low degree of order in this polymer, indicating the existence of interconnected crystal domains in the predominantly amorphous polymer matrix through which the charge was transported. We have thus shown that the addition of bulky pendant groups to conducting polymers does not prevent efficient charge transport via the residual scattering mechanism with low barriers to charge transport.

Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer.

We herein report the synthesis and electrochemical characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole, consisting of a polypyrrole backbone derivatized at the beta position by a vinyl-hydroquinone pendant group. The structure of the polymer was characterized by solid state NMR spectroscopy. The interactions between the polypyrrole backbone and the oxidized quinone or reduced hydroquinone pendant groups are probed by several in situ methods. In situ attenuated total reflectance-Fourier transform infrared spectroscopy shows a spectroscopic response from both the doping of the polymer backbone and the redox activity of the pendant groups. Using an in situ Electrochemical Quartz Crystal Microbalance we reveal that the polymer doping is unaffected by the pendant group redox chemistry, as opposed to previous reports. Despite the continuous doping the electrochemical conversion from the hydroquinone state to the quinone state results in a significant conductance drop, as observed by in situ conductivity measurements using an Interdigitated Array electrode set-up. Twisting of the conducting polymer backbone as a result of a decreased separation between pendant groups due to π-π stacking in the oxidized state is suggested as the cause of this conductance drop.

Air- and Light-Stable P4 and As4 within an Anion-Coordination-Based Tetrahedral Cage.

In contrast to the stable dinitrogen molecule, white phosphorus (P4) and yellow arsenic (As4) are very reactive allotropic modifications of these two heavier pnictogen elements, which has greatly hampered the study of their properties and applications. Thus, the safe storage and transport of them is imperative. Supramolecular caged structures are one of the most efficient approaches for the encapsulation and stabilization of reactive species; however, their use in the P4 and As4 chemistry is very rare. In the current work, we demonstrate a new design strategy for constructing finite cages and including guests based on anion coordination chemistry. The phosphate-coordination-based tetrahedral cages can readily accommodate the tetrahedral guests P4 and As4, which is facilitated by the shape and size complementarity as well as favorable σ-π and lone-pair-π interactions. Moreover, the latter case represents the first example of As4 inclusion in a well-defined tetrahedral cage.

Hydroquinone-pyrrole dyads with varied linkers.

A series of pyrroles functionalized in the 3-position with p-dimethoxybenzene via various linkers (CH2, CH2CH2, CH=CH, C≡C) has been synthesized. Their electronic properties have been deduced from (1)H NMR, (13)C NMR, and UV-vis spectra to detect possible interactions between the two aromatic subunits. The extent of conjugation between the subunits is largely controlled by the nature of the linker, with the largest conjugation found with the trans-ethene linker and the weakest with the aliphatic linkers. DFT calculations revealed substantial changes in the HOMO-LUMO gap that correlated with the extent of conjugation found experimentally. The results of this work are expected to open up for use of the investigated compounds as components of redox-active materials in sustainable, organic electrical energy storage devices.

A versatile route to polythiophenes with functional pendant groups using alkyne chemistry.

A new versatile polythiophene building block, 3-(3,4-ethylenedioxythiophene)prop-1-yne (pyEDOT) (3), is prepared from glycidol in four steps in 28% overall yield. pyEDOT features an ethynyl group on its ethylenedioxy bridge, allowing further functionalization by alkyne chemistry. Its usefulness is demonstrated by a series of functionalized polythiophene derivatives that were obtained by pre- and post-electropolymerization transformations, provided by the synthetic ease of the Sonogashira coupling and click chemistry.

Synthesis and Properties of Bis-Porphyrin Molecular Tweezers: Effects of Spacer Flexibility on Binding and Supramolecular Chirogenesis.

Ditopic binding of various dinitrogen compounds to three bisporphyrin molecular tweezers with spacers of varying conformational rigidity, incorporating the planar enediyne (1), the helical stiff stilbene (2), or the semi-rigid glycoluril motif fused to the porphyrins (3), are compared. Binding constants Ka = 104-106 M(-1) reveal subtle differences between these tweezers, that are discussed in terms of porphyrin dislocation modes. Exciton coupled circular dichroism (ECCD) of complexes with chiral dinitrogen guests provides experimental evidence for the conformational properties of the tweezers. The results are further supported and rationalized by conformational analysis.

Phototriggerable peptidomimetics for the inhibition of Mycobacterium tuberculosis ribonucleotide reductase by targeting protein-protein binding.

Incorporation of an artificial amino acid 2 with a stilbene chromophore into peptidomimetics with three to nine amino acids yields phototriggerable candidates for inhibition of the binding between the R1 and R2 subunits of the M. tuberculosis ribonucleotide reductase (RNR). Interstrand hydrogen bond probability was used as a guideline for predicting conformational preferences of the photoisomers. Binding of these inhibitors has been rationalized by docking studies with the R1 unit. Significant differences in binding of the photoisomers were observed. For the shorter peptidomimetics, stronger binding of the Z isomer might indicate hydrophobic interactions between the stilbene chromophore and the binding site.

Improved stereochemical analysis of conformationally flexible diamines by binding to a bisporphyrin molecular clip.

The relative stereochemistry of acyclic diamines with several stereogenic centers has been analyzed by NMR spectroscopy in combination with conformational deconvolution. Binding to a bisporphyrin molecular clip improves the stereochemical assignment significantly. The diamines were synthesized from inexpensive sugar alcohols, and their stable hydrochlorides were quantitatively converted into free bases by treatment with ion-exchange resin.

Protonation-triggered conformational modulation of an N,N'-dialkylbispidine: first observation of the elusive boat-boat conformer.

Modulation of the solution conformations of N,N'-bis(benzhydryl)bispidine has been achieved by protonation. Conformers have been characterized by NMR spectroscopy using nuclear Overhauser effects and residual dipolar couplings. In contrast to the preference for the chair-chair conformation for the free base and the monoprotonated species, the diprotonated bispidine is revealed to exist as a mixture of chair-boat and boat-boat conformers. While boat-boat conformers of bispidines have previously not been detected, they are here observed to constitute up to 70% of the bispidine population.

Formation and NMR spectroscopy of ω-thiol protected α,ω-alkanedithiol-coated gold nanoparticles and their usage in molecular charge transport junctions.

Gold nanoparticles (AuNPs) coated with stabilizing molecular monolayers are utilized in areas ranging from life sciences to nanoelectronics. Here we present a novel and facile one-pot single phase procedure for the preparation of stable AuNPs with good dispersity, which are coated with α,ω-alkanedithiols whose outer ω-thiol is protected by a triphenylmethyl group. Using dielectrophoresis we were able to trap these AuNPs, coated with ω-thiol protecting groups, in a 20 nm gold electrode nanogap. The ω-thiol group was then deprotected under acidic conditions in situ once the AuNPs were correctly positioned in the device. The subsequent deprotection resulted in an increase of conductance by up to 3 orders of magnitude, indicating that the isolated dithiol-coated AuNPs were fused into a covalently bonded network with AuNP-molecule-AuNP as well as electrode-molecule-AuNP linkages. Furthermore, complete characterization of the AuNP surface-bonded alkanedithiols was achieved using a series of one- and two-dimensional NMR spectroscopy techniques. Our spectra of the molecule-coated AuNPs show well-resolved signals, only slightly broader than for free molecules in solution, which is in contrast to many earlier reported NMR spectral data of molecules attached to AuNPs. Complementary diffusion NMR spectroscopic experiments were performed to prove that the observed alkanedithiols are definitely surface-bonded species and do not exist in free and unattached form.