New Polymethoxyflavones from Hottonia palustris Evoke DNA Biosynthesis-Inhibitory Activity in An Oral Squamous Carcinoma (SCC-25) Cell Line.

Four new compounds, 5-hydroxy-2',6'-dimethoxyflavone (4), 5-hydroxy-2',3',6'-trimethoxyflavone (5), 5-dihydroxy-6-methoxyflavone (6), and 5,6'-dihydroxy-2',3'-dimethoxyflavone (7), and three known compounds, 1,3-diphenylpropane-1,3-dione (1), 5-hydroxyflavone (2), and 5-hydroxy-2'-methoxyflavone (3), were isolated from the aerial parts of Hottonia palustris. Their chemical structures were determined through the use of spectral, spectroscopic and crystallographic methods. The quantitative analysis of the compounds (1-7) and the zapotin (ZAP) in methanol (HP1), petroleum (HP6), and two chloroform extracts (HP7 and HP8) were also determined using HPLC-PDA. The biological activity of these compounds and extracts on the oral squamous carcinoma cell (SCC-25) line was investigated by considering their cytotoxic effects using the MTT assay. Subsequently, the most active compounds and extracts were assessed for their effect on DNA biosynthesis. It was found that all tested samples during 48 h treatment of SCC-25 cells induced the DNA biosynthesis-inhibitory activity: compound 1 (IC50, 29.10 ± 1.45 µM), compound 7 (IC50, 40.60 ± 1.65 µM) and extracts ZAP (IC50, 20.33 ± 1.01 µM), HP6 (IC50, 14.90 ± 0.74 µg), HP7 (IC50, 16.70 ± 0.83 µg), and HP1 (IC50, 30.30 ± 1.15 µg). The data suggest that the novel polymethoxyflavones isolated from Hottonia palustris evoke potent DNA biosynthesis inhibitory activity that may be considered in further studies on experimental pharmacotherapy of oral squamous cell carcinoma.

Synthesis and Structural Characterization of Pyridine-2,6-dicarboxamide and Furan-2,5-dicarboxamide Derivatives.

Derivatives based on pyridine-2-6- and furan-2,5-dicarboxamide scaffolds reveal numerous chemical properties and biological activities. This fact makes them an exciting research topic in supramolecular and coordination chemistry and in discovering new pharmacologically-active compounds. This work aimed to obtain a series of symmetrical pyridine-2-6- and furan-2,5-dicarboxamides through a condensation reaction of the appropriate acyl chlorides and aromatic amides. Successful syntheses were confirmed with NMR spectroscopy. We solved their crystal structures for seven compounds; two pyridine and five furan derivatives. Based on our crystallographic studies, we were able to indicate supramolecular features of the crystals under investigation. Additionally, Hirshfeld surface analysis allowed us to calculate a distribution of intermolecular contacts in the dicarboxamide crystals.

Monocarbonyl Analogs of Curcumin Based on the Pseudopelletierine Scaffold: Synthesis and Anti-Inflammatory Activity.

Curcumin (CUR) is a natural compound that exhibits anti-inflammatory, anti-bacterial, and other biological properties. However, its application as an effective drug is problematic due to its poor oral bioavailability, solubility in water, and poor absorption from the gastrointestinal tract. The aim of this work is to synthesize monocarbonyl analogs of CUR based on the 9-methyl-9-azabicyclo[3.2.1]nonan-3-one (pseudopelletierine, granatanone) scaffold to improve its bioavailability. Granatane is a homologue of tropane, whose structure is present in numerous naturally occurring alkaloids, e.g., l-cocaine and l-scopolamine. In this study, ten new pseudopelletierine-derived monocarbonyl analogs of CUR were successfully synthesized and characterized by spectral methods and X-ray crystallography. Additionally, in vitro test of the cytotoxicity and anti-inflammatory properties of the synthesized compounds were performed.

New VIV, VIVO, VVO, and VVO2 Systems: Exploring their Interconversion in Solution, Protein Interactions, and Cytotoxicity.

The synthesis and characterization of one oxidoethoxidovanadium(V) [VVO(L1)(OEt)] (1) and two nonoxidovanadium(IV) complexes, [VIV(L2-3)2] (2 and 3), with aroylhydrazone ligands incorporating naphthalene moieties, are reported. The synthesized oxido and nonoxido vanadium complexes are characterized by various physicochemical techniques, and their molecular structures are solved by single crystal X-ray diffraction (SC-XRD). This revealed that in 1 the geometry around the vanadium atom corresponds to a distorted square pyramid, with a O4N coordination sphere, whereas that of the two nonoxido VIV complexes 2 and 3 corresponds to a distorted trigonal prismatic arrangement with a O4N2 coordination sphere around each "bare" vanadium center. In aqueous solution, the VVO moiety of 1 undergoes a change to VVO2 species, yielding [VVO2(L1)]- (1'), while the nonoxido VIV-compounds 2 and 3 are partly converted into their corresponding VIVO complexes, [VIVO(L2-3)(H2O)] (2' and 3'). Interaction of these VVO2, VIVO, and VIV systems with two model proteins, ubiquitin (Ub) and lysozyme (Lyz), is investigated through docking approaches, which suggest the potential binding sites: the interaction is covalent for species 2' and 3', with the binding to Glu16, Glu18, and Asp21 for Ub, and His15 for Lyz, and it is noncovalent for species 1', 2, and 3, with the surface residues of the proteins. The ligand precursors and complexes are also evaluated for their in vitro antiproliferative activity against ovarian (A2780) and prostate (PC3) human cancer cells and in normal fibroblasts (V79) to check the selectivity of the compounds for cancer cells.

Boron-Doped Polygonal Carbon Nano-Onions: Synthesis and Applications in Electrochemical Energy Storage.

Doping of carbon nanostructures with heteroatoms, such as boron or nitrogen, is one of the most effective ways to change their properties to make them suitable for various applications. Carbon nano-onions (CNOs) doped with boron (B-CNOs) were prepared by annealing (1650 °C) nanodiamond particles (NDs) under an inert He atmosphere in the presence of B. Their physicochemical properties were measured using transmission (TEM) and scanning (SEM) electron microscopy, X-ray photoelectron spectroscopy (XPS), 10 B and 11 B solid-state magic-angle spinning (MAS) NMR spectroscopy, X-ray powder diffraction (XRD), Raman spectroscopy, porosimetry, and differential-thermogravimetric analyses (TGA-DTG). These properties were systematically discussed for the undoped and B-doped CNO samples. The amount of substitutional B in the CNO samples varied from 0.76 to 3.21 at. %. The TEM, XRD, and Raman analyses revealed that the increased amount of B doping resulted in decreased interlayer spacing and polygonization of the structures, which in turn led to their unusual physicochemical properties. All synthesized materials were tested as electrodes for electrochemical capacitors. The B-CNOs with low concentration of doping agent exhibited higher reversible capacitances, mainly owing to the formation of hydrophilic polygonal nanostructures and higher porosity.

Chemistry of Monomeric and Dinuclear Non-Oxido Vanadium(IV) and Oxidovanadium(V) Aroylazine Complexes: Exploring Solution Behavior.

A series of mononuclear non-oxido vanadium(IV) [V(IV)(L(1-4))2] (1-4), oxidoethoxido vanadium(V) [V(V)O(L(1-4))(OEt)] (5-8), and dinuclear µ-oxidodioxidodivanadium(V) [V(V)2O3(L(1))2] (9) complexes with tridentate aroylazine ligands are reported [H2L(1) = 2-furoylazine of 2-hydroxy-1-acetonaphthone, H2L(2) = 2-thiophenoylazine of 2-hydroxy-1-acetonaphthone, H2L(3) = 1-naphthoylazine of 2-hydroxy-1-acetonaphthone, H2L(4) = 3-hydroxy-2-naphthoylazine of 2-hydroxy-1-acetonaphthone]. The complexes are characterized by elemental analysis, by various spectroscopic techniques, and by single-crystal X-ray diffraction (for 2, 3, 5, 6, 8, and 9). The non-oxido V(IV) complexes (1-4) are quite stable in open air as well as in solution, and DFT calculations allow predicting EPR and UV-vis spectra and the electronic structure. The solution behavior of the [V(V)O(L(1-4))(OEt)] compounds (5-8) is studied confirming the formation of at least two different types of V(V) species in solution, monomeric corresponding to 5-8, and µ-oxidodioxidodivanadium [V(V)2O3(L(1-4))2] compounds. The µ-oxidodioxidodivanadium compound [V(V)2O3(L(1))2] (9), generated from the corresponding mononuclear complex [V(V)O(L(1))(OEt)] (5), is characterized in solution and in the solid state. The single-crystal X-ray diffraction analyses of the non-oxido vanadium(IV) compounds (2 and 3) show a N2O4 binding set and a trigonal prismatic geometry, and those of the V(V)O complexes 5, 6, and 8 and the µ-oxidodioxidodivanadium(V) (9) reveal that the metal center is in a distorted square pyramidal geometry with O4N binding sets. For the µ-oxidodioxidodivanadium species in equilibrium with 5-8 in CH2Cl2, no mixed-valence complexes are detected by chronocoulometric and EPR studies. However, upon progressive transfer of two electrons, two distinct monomeric V(IV)O species are detected and characterized by EPR spectroscopy and DFT calculations.

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.

The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

Relative configuration, absolute configuration and absolute structure of three isomeric 8-benzyl-2-[(4-bromophenyl)(hydroxy)methyl]-8-azabicyclo[3.2.1]octan-3-ones.

The title compounds, C21H22BrNO2, are isomeric 8-benzyl-2-[(4-bromophenyl)(hydroxy)methyl]-8-azabicyclo[3.2.1]octan-3-ones. Compound (I), the (±)-exo,syn-(1RS,2SR,5SR,9SR) isomer, crystallizes in the hexagonal space group R-3, while compounds (II) [the (+)-exo,anti-(1R,2S,5S,9R) isomer] and (III) [the (±)-exo,anti-(1RS,2SR,5SR,9RS) isomer] crystallize in the orthorhombic space groups P212121 and Pna21, respectively. The absolute configuration was determined for enantiomerically pure (II). For the noncentrosymmetric crystal of (III), its absolute structure was established. In the crystal structures of (I) and (II), an intramolecular hydrogen bond is formed between the hydroxy group and the heterocyclic N atom. In the crystal structure of racemic (III), hydrogen-bonded chains of molecules are formed via intermolecular O-H...O interactions. Additionally, face-to-edge π-π interactions are present in the crystal structures of (I) and (II). In all three structures, the piperidinone rings adopt chair conformations and the N-benzyl substituents occupy the equatorial positions.

Tetra-ethyl-ammonium toluene-4-sulfon-ate.

There are two tetra-ethyl-ammonium cations and two toluene-4-sulfate anions in the asymmetric unit of the title salt, C8H20N(+)·C7H7O3S(-). One of the anions is disordered over two positions, with refined occupancies of 0.447 (3) and 0.553 (3). In the crystal, the cations and anions are linked by C-H⋯O hydrogen bonds, forming ribbons along [10-1]. The ribbons are linked via C-H⋯O hydrogen bonds, forming a two-dimensional network lying parallel to (10-1).

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of ß-D-Ribofuranose since the Origins of Life.

Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of ß-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of ß-d-ribofuranose instead of compounds based on other sugar moieties.

Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.

The self-complementary L-d(CGCGCG)2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Šresolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K+ cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K+ site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder.

Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members.

Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.

Three-dimensional organization of pyrrolo[3,2-b]pyrrole-based triazine framework using nanostructural spherical carbon: enhancing electrochemical performance of materials for supercapacitors.

Covalent triazine-based frameworks have attracted much interest recently due to their high surface area and excellent thermal and electrochemical stabilities. This study shows that covalently immobilizing triazine-based structures on spherical carbon nanostructures results in the organization of micro- and mesopores in a three-dimensional manner. We selected the nitrile-functionalized pyrrolo[3,2-b]pyrrole unit to form triazine rings to construct a covalent organic framework. Combining spherical carbon nanostructures with the triazine framework produced a material with unique physicochemical properties, exhibiting the highest specific capacitance value of 638 F g-1 in aqueous acidic solutions. This phenomenon is attributed to many factors. The material exhibits a large surface area, a high content of micropores, a high content of graphitic N, and N-sites with basicity and semi-crystalline character. Thanks to the high structural organization and reproducibility, and remarkably high specific capacitance, these systems are promising materials for use in electrochemistry. For the first time, hybrid systems containing triazine-based frameworks and carbon nano-onions were used as electrodes for supercapacitors.

High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).

S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a major regulator of SAM-dependent biological methylation reactions. Here, the first crystal structure of SAHase of plant origin, that from the legume yellow lupin (LlSAHase), is presented. Structures have been determined at high resolution for three complexes of the enzyme: those with a reaction byproduct/substrate (adenosine), with its nonoxidizable analog (cordycepin) and with a product of inhibitor cleavage (adenine). In all three cases the enzyme has a closed conformation. A sodium cation is found near the active site, coordinated by residues from a conserved loop that hinges domain movement upon reactant binding. An insertion segment that is present in all plant SAHases is located near a substrate-pocket access channel and participates in its formation. In contrast to mammalian and bacterial SAHases, the channel is open when adenosine or cordycepin is bound and is closed in the adenine complex. In contrast to SAHases from other organisms, which are active as tetramers, the plant enzyme functions as a homodimer in solution.

Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose.

Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-ß-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Šresolution. The fucose residue is exposed to solvent and is disordered. The enzyme-product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-L-glucosamine (penta-NAG). The structure has been determined at 1.98 Šresolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand ßC2 and helix αC3. In addition, there is a shift of the αC3 helix itself upon GDP-Fuc binding.

Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio.

PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Šby direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded ß-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel ß-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

(1RS,2SR,5SR)-9-Benzyl-2-[(1RS)-1-hy-droxy-benz-yl]-9-aza-bicyclo-[3.3.1]nonan-3-one from synchrotron data.

In the crystal structure of the racemic title compound, C(22)H(25)NO(2), solved and refined against sychrotron diffraction data, the hy-droxy group and the carbonyl O atom participate in the formation of O-H⋯O hydrogen bonds between pairs of enanti-omers related by a crystallographic centre of symmetry.

Tris(1,10-phenanthroline-κ(2) N,N')ruthenium(II) bis-(perchlorate).

The asymmetric unit of the title compound, [Ru(C12H8N2)3](ClO4)2, contains one octahedrally coordinated Ru(II) cation of the ruthenium-phenanthroline complex and three differently occupied perchlorate anions: two, denoted A and B, are located on the twofold axis while another, denoted C, is positioned in the proximity of the twofold screw axis. Perchlorate anions B and C are severely disordered. The occupancies of the two major conformers of anion B refined to 0.302 (6) and 0.198 (6). Perchlorate ion C was modeled in two alternate conformations which refined to occupancies of 0.552 (10) and 0.448 (10).

Bis(2,2':6',2''-terpyridine)-ruthenium(II) bis-(perchlorate) hemihydrate.

The asymmetric unit of the title compound, [Ru(C(15)H(11)N(3))(2)](ClO(4))(2)·0.5H(2)O, contains one ruthenium-terpiridine complex cation, two perchlorate anions and one half-mol-ecule of water. Face-to-face and face-to-edge π-stacking inter-actions between terpyridine units [centroid-centroid distances = 3.793 (2) and 3.801 (2)  Å] stabilize the crystal lattice The partially occupied water mol-ecule inter-acts with two perchlorate ions via O-H⋯O hydrogen bonds. In the crystal lattice, the complex cations, perchlorate ion-water pairs and the second perchlorate anions are arranged into columns along b direction.

(2R)-8-Benzyl-2-[(S)-hy-droxy(phen-yl)meth-yl]-8-aza-bicyclo-[3.2.1]octan-3-one.

The crystal of the title compound, C(21)H(23)NO(2), was chosen from a conglomerate formed by a racemic mixture. An intra-molecular hydrogen bond is formed between hy-droxy group and heterocyclic N atom of the aza-bicyclo-[3.2.1]octan-3-one system. The crystal structure is stabilized by C-H⋯O inter-actions between aliphatic C-H groups and the carbonyl O atom. For the title chiral crystal, the highly redundant and accurate diffraction data set collected with low energy copper radiation gave a Flack parameter of 0.12 (18) for anomalous scattering effects originating from O atoms.