Red Wine Inspired Chemistry: Hemisynthesis of Procyanidin Analogs and Determination of Their Protein Precipitation Capacity, Octanol-Water Partition, and Stability in Phosphate-Buffered Saline.

Ten dimeric procyanidin (PC) analogs were hemisynthesized from catechin or epicatechin and from five different aldehydes using the same mechanism that produces the important acetaldehyde-mediated adducts of proanthocyanidins (PAs) and anthocyanins in red wine. Protein precipitation capacity (PPC), octanol-water partition coefficient (log P) and stability of the PC analogs were determined. The emphasis was on the PPC because it has been shown to correlate with anthelmintic activity against gastrointestinal nematodes in ruminants and with other beneficial bioactivities in animals, as well. The PPC of PC analogs was greatly improved compared to natural PC dimers, but the capacity was not as great as that of a PC trimer or epigallocatechin gallate. The log P of PC analogs varied from hydrophobic to hydrophilic depending on the intramolecular linkage. Great variation was observed in stabilities of PC analogs in phosphate buffered saline, and the mixtures of degradation products were characterized using high-resolution mass spectrometry.

Tannins Can Have Direct Interactions with Anthelmintics: Investigations by Isothermal Titration Calorimetry.

Plant tannins are known for their anthelmintic and antiparasitic activities and have been increasingly studied to battle the ever-growing problem of anthelmintic resistance. While tannins have been shown to exhibit these activities on their own, one approach would be to use them as complementary nutrients alongside commercial anthelmintics. So far, research on the interactions between tannins and anthelmintics is limited, and few studies have reported both synergistic and antagonistic effects depending on the type of tannin and the method used. These interactions could either strengthen or weaken the efficacy of commercial anthelmintics, especially if tannin-rich diets are combined with anthelmintics used as oral drenches. To study these interactions, a series of hydrolysable tannins (HTs) was selected, and their direct interactions with thiabendazole (TBZ) were evaluated by isothermal titration calorimetry (ITC), which allowed the detection of the exothermic interaction but also the roles and significances of different structural features of HTs in these interactions. Our results show that HTs can have a direct interaction with the benzimidazole anthelmintic TBZ and that the interaction is strengthened by increasing the number of free galloyl groups and the overall molecular flexibility of HTs.

Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences.

Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.

Tautomers of N-acetyl-d-allosamine: an NMR and computational chemistry study.

d-Allosamine is a rare sugar in Nature but its pyranoid form has been found α-linked in the core region of the lipopolysaccharide from the Gram-negative bacterium Porphyromonas gingivalis and in the chitanase inhibitor allosamidin, then ß-linked and N-acetylated. In water solution the monosaccharide N-acetyl-d-allosamine (d-AllNAc) shows a significant presence of four tautomers arising from pyranoid and furanoid ring forms and anomeric configurations. The furanoid ring forms both showed 3JH1,H2≈ 4.85 Hz and to differentiate the anomeric configurations a series of chemical shift anisotropy/dipole-dipole cross-correlated relaxation NMR experiments was performed in which the α-anomeric form showed notable different relaxation rates for its components of the H1 doublet, thereby making it possible to elucidate the anomeric configuration of each of the furanoses. The conformational preferences of the different forms of d-AllNAc were investigated by 3JHH, 2JCH and 3JCH coupling constants from NMR experiments, molecular dynamics simulations and density functional theory calculations. The pyranose form resides in the 4C1 conformation and the furanose ring form has the majority of its conformers located on the South-East region of the pseudorotation wheel, with a small population in the Northern hemisphere. The tautomeric equilibrium was quite sensitive to changes in temperature, where the ß-anomer of the pyranoid ring form decreased upon a temperature increase while the other forms increased.

Kinetic and NMR spectroscopic study of the chemical stability and reaction pathways of sugar nucleotides.

The alkaline cleavage of two types of sugar nucleotides has been studied by 1H and 31P NMR in order to obtain information on the stability and decomposition pathways in aqueous solutions under alkaline conditions. The reaction of glucose 1-UDP is straightforward, and products are easy to identify. The results obtained with ribose 5-UDP and ribose 5-phosphate reveal, in contrast, a more complex reaction system than expected, and the identification of individual intermediate species was not possible. Even though definite proof for the mechanisms previously proposed could not be obtained, all the spectroscopic evidence is consistent with them. Results also emphasise the significant effect of conditions, pH, ionic strength, and temperature, on the reactivity under chemical conditions.

1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase.

A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔTm =7.3 °C) HgII -mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two HgII ions coordinated to O2 and O4 of the thymine base.

New Sulfur-Containing Polyarsenicals from the New Caledonian Sponge Echinochalina bargibanti.

Arsenicin A (C3H6As4O3) was isolated from the New Caledonian poecilosclerid sponge Echinochalina bargibanti, and described as the first natural organic polyarsenic compound. Further bioguided fractionation of the extracts of this sponge led us to isolate the first sulfur-containing organic polyarsenicals ever found in Nature. These metabolites, called arsenicin B and arsenicin C, are built on a noradamantane-type framework that is characterized by an unusual As⁻As bonding. Extensive NMR measurements, in combination with mass spectra, enabled the assignment of the structure for arsenicin B (C3H6As4S2) as 2. The scarcity of arsenicin C and its intrinsic chemical instability only allowed the collection of partial spectral data, which prevented the full structural definition. After the extensive computational testing of several putative structures, structure 3 was inferred for arsenicin C (C3H6As4OS) by comparing the experimental and density functional theory (DFT)-calculated ¹H and 13C NMR spectra. Finally, the absolute configurations of 2 and 3 were determined with a combined use of experimental and time-dependent (TD)-DFT calculated electronic circular dichroism (ECD) spectra and observed specific rotations. These findings pose great challenges for the investigation of the biosynthesis of these metabolites and the cycle of arsenic in Nature. Arsenicins B and C showed strong antimicrobial activities, especially against S. aureus, which is comparable to the reference compound gentamycin.

Isolation of chemically well-defined semipreparative liquid chromatography fractions from complex mixtures of proanthocyanidin oligomers and polymers.

In this study, a semipreparative liquid chromatography method was developed for the isolation of chemically well-defined proanthocyanidin (PA) oligomer and polymer fractions. The aim was to achieve better separation than traditionally achieved for the PAs with other chromatographic methods. The method was tested with eleven PA rich Sephadex LH-20 fractions, which originated from eleven different plant species. The resulting semipreparative fractions were analyzed by both triple quadrupole and high-resolution mass spectrometry assisted by ultrahigh-performance liquid chromatography (UPLC) separation. The results showed remarkable differences in the procyanidin to prodelphinidin ratio, mean degree of polymerization, and specific oligomeric and polymeric content. However, some of these features indicated consistent patterns between species as the function of UPLC retention time. The developed method enables the production of tens of well-defined fractions of PA oligomers and polymers from the unresolved chromatographic PA hump. Accordingly, this allows researchers to explore the most bioactive parts of the complex PA humps of any plant species, which have not been possible earlier.

Variability in Foliar Ellagitannins of Hippophaë rhamnoides L. and Identification of a New Ellagitannin, Hippophaenin C.

Berries of common sea-buckthorn (Hippophaë rhamnoides L.) are well-known and used for their bioactive components, and while there is a considerable amount of research on the leaves as well, their ellagitannins (ETs) have not been a prominent focus of research. We identified and quantified ten major hydrophilic polyphenols, all ETs, in H. rhamnoides leaves and compared their abundance between 58 plant individuals. Of these compounds, hippophaenin C was characterized as a new ellagitannin by various spectrometric methods. The total concentrations of ETs ranged from 42.5 mg g-1 dry weight (DW) to 109.1 mg g-1 DW between individual plants. Among the ETs, hippophaenin C, stachyurin, and casuarinin were on average the most abundant compounds. Sexes did not differ significantly, while cultivars showed variation in some ETs. These results suggest that H. rhamnoides leaves could be a potential and rich source of several ETs.

Biological activity of ellagitannins: Effects as anti-oxidants, pro-oxidants and metal chelators.

Ellagitannins are a subclass of hydrolysable tannins that have been suggested to function as defensive compounds of plants against herbivores. However, it is known that the conditions in the digestive tracts of different herbivores are variable, so it seems reasonable to anticipate that the reactivities and modes of actions of these ingested defensive compounds would also be different. A previous study on a few ellagitannins has shown that these polyphenolic compounds are highly oxidizable at high pH and that their bioactivity can be attributed to certain structural features. Herein, the activities of 13 ellagitannins using the deoxyribose assay were measured. The results provided information about the anti-oxidant, pro-oxidant and metal chelating properties of ellagitannins. Surprisingly, many of the tested ellagitannins exhibited pro-oxidant activities even at neutral pH and only moderate to low radical scavenging activities, although the metal chelating capacities of all tested ellagitannins were relatively high.

Phenolic Compounds and Their Fates In Tropical Lepidopteran Larvae: Modifications In Alkaline Conditions.

Lepidopteran larvae encounter a variety of phenolic compounds while consuming their host plants. Some phenolics may oxidize under alkaline conditions prevailing in the larval guts, and the oxidation products may cause oxidative stress to the larvae. In this study, we aimed to find new ways to predict how phenolic compounds may be modified in the guts of herbivorous larvae. To do so, we studied the ease of oxidation of phenolic compounds from 12 tropical tree species. The leaf extracts were incubated in vitro in alkaline conditions, and the loss of total phenolics during incubation was used to estimate the oxidizability of extracts. The phenolic profiles of the leaf extracts before and after incubation were compared, revealing that some phenolic compounds were depleted during incubation. The leaves of the 12 tree species were each fed to 12 species of lepidopteran larvae that naturally feed on these trees. The phenolic profiles of larval frass were compared to those of in vitro incubated leaf extracts. These comparisons showed that the phenolic profiles of alkali-treated samples and frass samples were similar in many cases. This suggested that certain phenolics, such as ellagitannins, proanthocyanidins, and galloylquinic acid derivatives were modified by the alkaline pH of the larval gut. In other cases, the chromatographic profiles of frass and in vitro incubated leaf extracts were not similar, and new modifications of phenolics were detected in the frass. We conclude that the actual fates of phenolics in vivo are often more complicated than can be predicted by a simple in vitro method.

Structure-based engineering of angucyclinone 6-ketoreductases.

Angucyclines are tetracyclic polyketides produced by Streptomyces bacteria that exhibit notable biological activities. The great diversity of angucyclinones is generated in tailoring reactions, which modify the common benz[a]anthraquinone carbon skeleton. In particular, the opposite stereochemistry of landomycins and urdamycins/gaudimycins at C-6 is generated by the short-chain alcohol dehydrogenases/reductases LanV and UrdMred/CabV, respectively. Here we present crystal structures of LanV and UrdMred in complex with NADP(+) and the product analog rabelomycin, which enabled us to identify four regions associated with the functional differentiation. The structural analysis was confirmed in chimeragenesis experiments focusing on these regions adjacent to the active site cavity, which led to reversal of the activities of LanV and CabV. The results surprisingly indicated that the conformation of the substrate and the stereochemical outcome of 6-ketoreduction appear to be intimately linked.

Flavonoid metabolites in the hemolymph of European pine sawfly (Neodiprion sertifer) larvae.

Flavonoids in the hemolymph of European pine sawfly (Neodiprion sertifer) larvae that were feeding on Pinus sylvestris needles were identified. HPLC-ESI-MS analysis revealed that the main components in the hemolymph were flavonol di- and triglucosides and a catechin monoglucoside. These compounds were isolated from the larval hemolymph and their structures were established by HPLC-MS, GC-MS, and NMR spectroscopy. The isolated flavonoids were identified as (+)-catechin 7-O-ß-glucoside, isorhamnetin 3,7,4'-tri-O-ß-glucoside, kaempferol 3,7,4'-tri-O-ß-glucoside, and quercetin 3,7,4'-tri-O-ß-glucoside. The combined concentration of these four compounds in the hemolymph was 3.7 mg/ml. None of these compounds was present in the needles of P. sylvestris. Therefore, we propose that the flavonoid glucosides were produced by the larvae from flavonoid monoglucosides and (+)-catechin obtained from the pine needles.

Computational NMR spectroscopy of organoarsenicals and the natural polyarsenic compound arsenicin A.

The (1)H and (13)C NMR chemical shifts and coupling constants of a series of organoarsenic compounds were calculated with DFT methods and compared with available experimental spectra. We show that non-relativistic methods successfully model the NMR spectra of these molecules; relativistic spin-orbit effects are small but appreciable for (13)C shifts, and their inclusion is beneficial. Application of the same methods of calculation to the intriguing natural polyarsenic compound arsenicin A allowed several viable alternative structures to be ruled out and thereby confirmed the previously suggested adamantane-like structure of arsenicin A. These results not only reinforce the known predictive power of DFT NMR calculations, but also open the way for the investigation of other naturally occurring molecules with unusual structures outside the scope of empirical methods.

Complete assignments of the (1)H and (13)C chemical shifts and J(H,H) coupling constants in NMR spectra of D-glucopyranose and all D-glucopyranosyl-D-glucopyranosides.

Complete assignment of the (1)H and (13)C NMR spectra of all possible d-glucopyranosyl-d-glucopyranosides was performed and the (1)H chemical shifts and proton-proton coupling constants were refined by computational spectral analyses (using PERCH NMR software) until full agreement between the calculated and experimental spectra was achieved. To support the experimental results, the (1)H and (13)C chemical shifts and the spin-spin coupling constants between the non-hydroxyl protons of alpha- and beta-d-glucopyranose (1a and 1b) were calculated with density functional theory (DFT) methods at the B3LYP/pcJ-2//B3LYP/6-31G(d,p) level of theory. The effects of different glycosidic linkage types and positions on the glucose ring conformations and on the alpha/beta-ratio of the reducing end hydroxyl groups were investigated. Conformational analyses were also performed for anomerically pure forms of methyl d-glucopyranosides (13a and 13b) and fully protected derivatives such as 1,2,3,4,6-penta-O-acetyl-d-glucopyranoses (14a and 14b).

Conformation of the galactose ring adopted in solution and in crystalline form as determined by experimental and DFT 1H NMR and single-crystal X-ray analysis.

The solution-state conformations of various galactose derivatives were determined by comparison of the experimental (1)H-(1)H vicinal coupling constants to those calculated using density functional theory (DFT) at the B3LYP/cc-pVTZ//B3LYP/6-31G(d,p) level of theory. The agreement between the experimental and calculated vicinal coupling constants for 1,2:3,4-di-O-isopropylidene-alpha-d-galactopyranose was good, thereby confirming an (O)S(2) skew conformation for it and its derivatives on the basis of their similar observed couplings. Single-crystal X-ray analysis of 1,2:3,4-di-O-isopropylidene-6-O-(3,4,6-tri-O-acetyl-2-deoxy-2-N-phthalimido-beta-d-glucopyranosyl)-alpha-d-galactopyranose and 1,2,3,4,6-penta-O-acetyl-alpha-d-galactopyranose provided (O)S(2) and (4)C(1) conformations, respectively, for the galactose ring in the solid state. The solid-state structures proved to be suitable starting structures for further DFT structure refinement or for immediate calculation of the coupling constants.

Experimental and DFT 1H NMR study of conformational equilibria in trans-4',7-dihydroxyisoflavan-4-ol and trans-isoflavan-4-ol.

The solution-state conformational equilibria of trans-4',7-dihydroxyisoflavan-4-ol (1) and trans-isoflavan-4-ol (2) were assessed based on the temperature dependence of their vicinal coupling constants J(H)(-)(2)(alpha)(,H)(-)(3) and J(H-3,H)(-)(4) in comparison to values calculated with density functional theory (DFT) methods at the B3LYP/cc-pVTZ//B3LYP/6-31G(d,p) level of theory. For each half-chair conformer, several rotamers with respect to the C-4 hydroxyl and C-3 phenyl were calculated and the overall diequatorial-to-diaxial ratio at 298 K was assessed as 66:34 for 1 and 73:27 for 2. The syntheses of 1 and 2 are described.

Modeling NMR parameters by DFT methods as an aid to the conformational analysis of cis-fused 7a(8a)-methyl octa(hexa)hydrocyclopenta[d][1,3]oxazines and [3,1]benzoxazines.

The energies of the preferred conformations of four 7a-methyl octa(or hexa)hydrocyclopenta[d][1,3]oxazines, five 8a-methyl octa(or hexa)hydro[3,1]benzoxazines, and 8a-methyl hexahydro[1,3]benzoxazinone, all cis-fused, were investigated by DFT methods. Following geometry optimization at the B3LYP/6-31G(d,p) level, both the proton chemical shifts and the vicinal coupling constants between H-4a and the H-4 and H-5 protons were calculated at the B3LYP/cc-pVTZ level and compared to the previously experimentally measured values. The agreement between the calculated and the experimental chemical shifts was found to be good. Similarly, the agreement between the calculated and the experimental vicinal coupling constants was also found to be good, thus providing a methodology for determining the conformational equilibria of such systems that is comparable in many respects to experimental approaches such as variable-temperature NMR or to the use of model coupling constant values, when available, from analogous compounds.

1H, (13)C, and (15)N NMR stereochemical study of cis-fused 7a(8a)-methyl and 6-phenyl octa(hexa)hydrocyclopenta[d][1,3]oxazines and [3,1]benzoxazines.

Four 7a-methyl octa(or hexa)hydrocyclopenta[d][1,3]oxazines, five 8a-methyl octa(or hexa)hydro[3,1]benzoxazines, two 6-phenyl hexahydro[3,1]benzoxazinones, and 8a-methyl hexahydro[1,3]benzoxazinone, all cis-fused, were prepared and their stereostructures studied by various one- and two-dimensional (1)H, (13)C, and (15)N NMR spectroscopic methods. In solution, the cyclopentane-fused 2-oxo derivatives and the 1,3-benzoxazinone were found to attain exclusively the N-in/O-in conformation, whereas the 6-phenyl 2-oxo/thioxo derivatives were found to be present predominantly in the N-out conformation. The C-2 unsubstituted and the 2-oxo/thioxo 7a/8a-methyl derivatives were all present in solution as a rapidly interconverting equilibrium of the N-in and N-out conformations. The C-2 methyl derivatives were each found to be interconvertable mixtures of epimers (at C-2) with the N-in conformer predominating for one epimer and the N-out conformer predominating for the other, with both predominating conformers having the C-2 methyl group equatorially orientated. The substituent on the nitrogen (H or Me) was found to be always predominantly equatorial with respect to the heteroring, except for the epimeric 2-methyl derivatives with N-out conformations where steric constraints and the generalized anomeric effect resulted in the axial orientation of the C-2 methyl being favored.

Conformational Study of Some Saturated 2-[Bis(2-chloroethyl)amino]-1,3,2-benzoxazaphosphorinane 2-Oxides.

Conformational analyses of cis- and trans-fused 2-[bis(2-chloroethyl)amino]-3,4,4a,5,6,7,8,8a-octahydro-1,3,2-benzoxazaphosphorinane 2-oxides and their 3-methyl and 3-benzyl derivatives were performed by (1)H, (13)C, (31)P, and variable-temperature NMR methods. Depending on the P-2 configuration and the substituent on N-3, different equilibria between chair-chair and chair-twist-boat conformations were found for the trans-fused isomers. The N-3 substituent shifts the equilibrium toward the chair-twist-boat to an extent varying in the sequence methyl > benzyl > hydrogen. In the cis-fused isomers, the nature of the N-3 substituent affects the equilibrium between the O-in and O-out conformations in the same sequence.