Synthesis and antimicrobial evaluation of 2-hydroxynaphthalene-1,4-dione and 4<Emphasis Type="Italic">H</Emphasis>-chromene conjugates

4H-Chromene and 1,4-naphthoquinone systems are generally considered to be medicinally privileged scaffolds. We have designed novel conjugates that incorporated both these scaffolds, as such conjugates exhibit unique biological properties reflecting those due to individual units and collective presence. In this work, we have achieved facile, efficient, and high yielding synthesis of 19 such conjugates from readily available 2-alkylamino-4-methylsulfanyl-3-nitro-4H-chromenes and 2-hydroxynaphthalene-1,4-dione. Highly polar nitroketene-O,N-acetal unit present in the conjugates is designed to prevent crossing blood brain barrier. We have conducted structure activity relationship (SAR) studies based on initial antimicrobial screening of a set of ten conjugates against three Gram positive bacteria [Bacillus Subtilis, Staphylococcus aureus (MSSA), Staphylococcus Escherichia coli), and two fungi (Aspergillus niger, Candida albicans). The SAR studies revealed that the conjugates with halogens at C(6) and C(8) positions of the 4H-chromene ring having C(2)NMe group display impressive activity, almost equal to that of standard drugs. None of the conjugates, however, showed antimalarial activity, although they possess 2-hydroxy-1,4-naphthoquinone unit.     

Quantum chemical studies of azoles 3. Thermodynamic stabilities of neutral molecules and intermediates formed in electrophilic substitution of azoles containing three or four heteroatoms

Density functional theory quantum chemical calculations of thermodynamic stabilities in the gas phase and in water were carried out for 1,3,4-oxadiazole and 1,3,4-thiadiazole, 1,2,4-1H-triazole and 1,2,4-4H-triazole, 1,2,3,4-1H-tetrazole and 1,2,3,4-2H-tetrazole molecules, and for cationic and bipolar (carbenoid) intermediates formed by these molecules in electrophilic substitution reactions (with proton as model electrophile) and the results obtained are compared. Differences in the chemical behavior of pairs of isomeric 1H- and 4H-1,2,4-triazoles and 1H- and 2H-tetrazoles are analyzed.     

Synthesis,Spectroscopic and Computational Studies of CT Complexes of Amino Acids with Iodine as σ Acceptor

Understanding the charge transfer process between bioactive molecules and inorganic or organic molecules is significant as this interaction can be used to interpret bioactive molecule–receptor interactions. A comprehensive spectrophotometric study has been performed to explore the complexation chemistry of the amino acids, tyrosine, lysine and arginine, with iodine as σ acceptor. The molecular structure, spectroscopic characteristics and the interactive modes have been deduced from UV–Vis and IR spectra. The binding ratio of complexation has been determined to be 1:1 for iodine with the amino acids. The association constant (K), extinction coefficient (ε _max), ionization potential (IP), energy of the charge transfer complex (E _CT), resonance energy (R _N ), dissociation energy (W) and standard Gibbs energy (ΔG°) have been computed. An in silico study has been carried out using GAMESS computations to understand the structural features. Highest occupied molecular orbital and lowest unoccupied molecular orbital calculations helped us in characterizing the chemical reactivity and kinetic stability of the molecules. A good consistency between experimental and computational results has been found.     

Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

Representing the 3D structures of ligands in virtual screenings via multi-conformer ensembles can be computationally intensive, especially for compounds with a large number of rotatable bonds. Thus, reducing the size of multi-conformer databases and the number of query conformers, while simultaneously reproducing the bioactive conformer with good accuracy, is of crucial interest. While clustering and RMSD filtering methods are employed in existing conformer generators, the novelty of this work is the inclusion of a clustering scheme (NMRCLUST) that does not require a user-defined cut-off value. This algorithm simultaneously optimizes the number and the average spread of the clusters. Here we describe and test four inter-dependent approaches for selecting computer-generated conformers, namely: OMEGA, NMRCLUST, RMS filtering and averaged-RMS filtering. The bioactive conformations of 65 selected ligands were extracted from the corresponding protein:ligand complexes from the Protein Data Bank, including eight ligands that adopted dissimilar bound conformations within different receptors. We show that NMRCLUST can be employed to further filter OMEGA-generated conformers while maintaining biological relevance of the ensemble. It was observed that NMRCLUST (containing on average 10 times fewer conformers per compound) performed nearly as well as OMEGA, and both outperformed RMS filtering and averaged-RMS filtering in terms of identifying the bioactive conformations with excellent and good matches (0.5 < RMSD < 1.0 Å). Furthermore, we propose thresholds for OMEGA root-mean square filtering depending on the number of rotors in a compound: 0.8, 1.0 and 1.4 for structures with low (1–4), medium (5–9) and high (10–15) numbers of rotatable bonds, respectively. The protocol employed is general and can be applied to reduce the number of conformers in multi-conformer compound collections and alleviate the complexity of downstream data processing in virtual screening experiments.     

Cycloascauloside b from <Emphasis Type="Italic">Astragalus caucasicus</Emphasis>

The structure of a new cycloartane glycoside isolated from leaves of Astragalus caucasicus Pall. (Leguminosae) was elucidated using chemical transformations and spectral data. Cycloascauloside B is 20R, 25-epoxy-24S-cycloartan-3β,6α,16β,24-tetraol 3-O-[α-L-rhamnopyranosyl-(1å2)]-β-D-glucopyranoside.     

Analysis of Novel Antioxidant Sesquarterpenes (C<Subscript>35</Subscript> Terpenes) Produced in Recombinant <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>

Novel synthetic isoprenoids have been synthesized in engineered microbial hosts by evolving terpene synthase or expressing heterologous terpene synthases. Recently, the native operon, crtN_aN_cM derived from Planococcus sp. PAMC 21323, has isolated for potential industrial applications of C₃₅ carotenoids. For the first time, novel C₃₅ carotenoids (sesquarterpene) were synthesized in Corynebacterium glutamicum expressing the crtN_aN_cM genes. The recombinant strains accumulate various sesquarterpene including 4-apolycopene (red color), 4-aponeurosporene (yellow color), and no pigmentation, depending on the expression of the genetic elements of the crtN_aN_cM genes. Subsequently, the carotenoid extract from the cells harboring pCES-H36-CrtN_aN_cM was analyzed, resulting in significantly higher antioxidant activity than those of other strains harboring pCES-H36-CrtN_cM and pCES-H36-CrtN_aN_c, respectively. This study will promote further engineering of C. glutamicum to increase sesquarterpene productions.     

Dissociation Constants of Silanol Groups of Silic Acids: Quantum Chemical Estimations

Dissociation constants of silanol groups on the silica surface are calculated with the DFT quantum chemical method using B3LYP and M06 functionals. Structural features of silanol fragments and the presence of hydrogen-bonded water clusters are shown to have significant effects on pK_a values of silanol groups. In particular, pK_a values are shown to vary widely depending on the features of the system of hydrogen bonds.     

Composition of essential oils of four <Emphasis Type="Italic">Hedychium</Emphasis>species from Vietnam

Background

Vietnam is a country blessed with many medicinal plants widely used as food and for medicinal purposes, and they contain a host of active substances that contribute to health. However, the analysis of chemical constituents of these plant species has not been subject of literature discussion.

Results

In this study, the chemical compositions of essential oils of four Hedychium species, obtained by hydrodistillation, were determined by means of gas chromatography-flame ionization detector (GC-FID) and gas chromatography–mass spectrometry (GC-MS) techniques. Individually, α-pinene (52.5%) and β-pinene (31.8%) were present in the leaf oil of Hedychium stenopetalum Lodd., while linalool (45.2%), (E)-nerolidol (8.7%) and α-pinene (5.0%) were identified in the root. The leaf of Hedychium coronarium J. König was characterized by α-pinene (20.0%), linalool (15.8%), 1,8-cineole (10.7%), α-pinene (10.1%) and α-terpineol (8.6%); while α-pinene (23.6%), α-humulene (17.1%) and β-caryophyllene (13.0%) were identified in the root. Hedychium flavum Roxb., gave oil whose major compounds were α-pinene (22.5%), α-humulene (15.7%) and β-caryophyllene (10.4%) in the leaf; α-humulene (18.9%), β-caryophyllene (11.8%) and α-pinene (11.2%) in the stem, as well as α-pinene (21.8%), linalool (17.5%) and 1,8-cineole (13.5%) in the root. The main constituents of Hedychium ellipticum Buch.-Ham. ex Smith were (E)-nerolidol (15.9%), α-pinene (11.8%) and bornyl acetate (9.2%) in the leaf with 1,8-cineole (40.8%), α-pinene (18.3%) and α-pinene (11.0%) occurring in the root.

Conclusions

Ubiquitous monoterpenes and sesquiterpenes were identified as characteristic markers for Hedychium species. This work is of great importance for the evaluation of Hedychium essential oils grown in Vietnam.

     

Kinetics of the Acid-Base Interaction between Tetra(4-<Emphasis Type="Italic">tert</Emphasis>-butyl)phthalocyanine and Nitrogen-Containing Bases in Dimethyl Sulfoxide

Specific features of the acid-base interaction of tetra(4-tert-butyl)phthalocyanine with cyclic and acyclic nitrogen-containing bases in dimethyl sulfoxide are studied. The effect of pK _a of proton-withdrawing molecules, basicity of a medium, and steric screening of acidic NH centers on the kinetic parameters of formation of proton-transfer complexes stable in time is shown.     

Description of the even-odd alternation of the clearing temperatures over homologous series of mesogens by second-order differential equations

It is shown for liquid crystals of various chemical classes that the nematic-isotropic transition temperatures in homologous series of compounds undergoing enantiotropic transitions are described by secondorder inhomogeneous recurrent equations with constant coefficients: T(n + 2) = aT(n + 1) + bT(n) + c (n is the number of alkyl carbon atoms). Solutions of the corresponding differential equations as T(n) functions allow reproduction of the even-odd alternation of the clearing temperatures.     

Thermodynamic properties of triphenylantimony dibenzoate

The temperature dependence of the heat capacity of triphenylantimony dibenzoate Ph₃Sb(OC(O)Ph)₂ is studied in the range of 6–480 K by means of precision adiabatic vacuum calorimetry and differential scanning calorimetry. The melting of the compound is observed in this temperature range, and its standard thermodynamic characteristics are identified and analyzed. Ph₃Sb(OC(O)Ph)₂ is obtained in a metastable amorphous state in a calorimeter. The standard thermodynamic functions of Ph₃Sb(OC(O)Ph)₂ in the crystalline and liquid states are calculated from the obtained experimental data: C_p^°(T), H°(T)–H°(0), S°(T), and G°(T)–H°(0) for the region from T → 0 to 480 K. The standard entropy of formation of the compound in the crystalline state at T = 298.15 K is determined. Multifractal processing of the low-temperature (T < 50 K) heat capacity of the compound is performed. It is concluded that the structure of the compound has a planar chain topology.     

Thermodynamic properties of a liquid crystal carbosilane dendrimer

The temperature dependence of the heat capacity of a first-generation liquid crystal carbosilane dendrimer with methoxyphenyl benzoate end groups is studied for the first time in the region of 6–370 K by means of precision adiabatic vacuum calorimetry. Physical transformations are observed in this interval of temperatures, and their standard thermodynamic characteristics are determined and discussed. Standard thermodynamic functions C_p^°(T), H°(T) ? H°(0), S°(T) ? S°(0), and G°(T) ? H°(0) are calculated from the obtained experimental data for the region of Т → 0 to 370 K. The standard entropy of formation of the dendrimer in the partially crystalline state at Т = 298.15 K is calculated, and the standard entropy of the hypothetic reaction of its synthesis at this temperature is estimated. The thermodynamic properties of the studied dendrimer are compared to those of second- and fourth-generation liquid crystal carbosilane dendrimers with the same end groups studied earlier.     

Synthesis,structure, and magnetic properties of magnesium bis-3,6-di-<Emphasis Type="Italic">tert</Emphasis>-butyl-<Emphasis Type="Italic">о</Emphasis>-benzosemiquinonate complexes with N-donor ligands

A series of six-coordinate magnesium bis-3,6-di-tert-butyl-о-benzosemiquinonate complexes with different N-donor ligands (2,2´-dipyridyl, 1,10-phenanthroline, 2,9-dimethyl-1,10-phenanthroline, pyridine, N-phenyl-1-(4-pyridinyl)methanimine) were synthesized. The molecular and crystal structures of these complexes were determined by X-ray diffraction. In the complexes with bidentate N-donor ligands, the O,O-diolate o-semiquinone ligands are cis to each other, whereas the compounds with monodentate ligands contain organic radical anions in trans positions. The specific features of magnetic exchange coupling between organic radical ligands were studied by temperature-dependent magnetic susceptibility measurements.     

Dual Stereochemical Control in Reaction of Di- and Trialkyl Phosphites with Aldimines

Stereochemistry of addition of di- and trialkyl phosphites to C=N compounds was investigated. Reactions of achiral dialkyl phosphites with chiral aldimines as well as that of chiral di-(1R,2S,5R)-menthyl phosphite with achiral aldimines result in low diastereomeric enrichment of the addition compound. Reaction stereoselectivity increased when supplementary chiral inductor was introduced to the reaction system. Reaction of di-(1R,2S, 5R)-menthyl phosphite with (S)-α-methylbenzylbenzaldimine proceeds as concerted asymmetric induction to form practically one diastereomer of N-substituted aminophosphonic acid. However, reaction of di-(1R,2S, 5R)-menthyl phosphite with (R)-α-methylbenzylbenzaldimine proceeded as not concerted asymmetric induction, and diastereomeric enrichment of the product was low. By chemical extrapolation, absolute configuration of compounds formed was established. Tri-(1R,2S,5R)-menthyl phosphite reacts with C=N compounds in the presence of boron trifluoride etherate to form aminophosphonic acid derivatives with the absolute configuration opposite to that appearing in the reaction of di-(1R,2S,5R)-menthyl phosphite with the same C=N compounds.     

Discovery of novel inhibitors for <Emphasis Type="Italic">Leishmania</Emphasis> nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization

Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl₂. It belongs to the hexagonal space group P6₃22 with unit cell parameters a?=?b?=?115.18, c?=?62.18 Å and α?=?β?=?90°, γ?=?120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R_free values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.     

Cre/loxP-Mediated Multicopy Integration of the Mevalonate Operon into the Genome of <Emphasis Type="Italic">Methylobacterium extorquens</Emphasis> AM1

Methylobacterium extorquens AM1 is the model strain for methylotrophic bacteria that metabolize methanol as the sole carbon and energy source. Genetically modified M. extorquens AM1 is used as a methylotrophic cell factory (MeCF) for high value-added chemical production. We tested the Cre-loxP recombination system for its ability to mediate multicopy gene integration of the mvt3 operon (mvt3) in M. extorquens AM1. mvt3 controls the expression of the first three enzymes of the mevalonate synthesis pathway. We assayed for Cre-mediated multigene integration by screening for multicopy mutants via their survival in culture with a high kanamycin concentration (600 μg/mL). We identified mutant strains in which the mevalonate titer was increased by up to 1.9-fold compared with M2 (M. extorquens AM1ΔcelABCΔattTn7::mvt3::loxP) and confirmed mvt3 integration at 2–3 copies per genome. This result demonstrates the feasibility of multicopy integration in M. extorquens AM1 mediated by Cre-loxP recombination and its potential for improving the output of M. extorquens AM1 metabolic pathways, e.g., optimization of terpenoid synthesis.     

Solution Thermodynamics of <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis><Superscript>/</Superscript>-Ethylenebis-(salicylideneiminato)-diaquochromium(III) Chloride in Aqueous Dimethylsulphoxide

The densities, viscosities and refractive indices of N,N ^/-ethylene-bis(salicylideneiminato)-diaquochromium(III) chloride, [Cr(salen)(H₂O)₂]Cl, in aqueous dimethylsulfoxide (DMSO) with different mass fractions (w ₂ = 0.20, 0.40, 0.60, 0.80 and 1.00) of DMSO were determined at 298.15, 308.15 and 318.15 K under atmospheric pressure. From measured densities, viscosities and refractive indices the apparent molar volumes (V _φ ), standard partial molar volume (V _φ ⁰ ), the slope (S _V ^* ), standard isobaric partial molar expansibility (φ _E ⁰ ) and its temperature dependence (?φ _E ⁰ /?T) _p , the viscosity B-coefficient, its temperature dependence (?B/?T), solvation number (S _n ) and apparent molar refractivity (R _D ^φ ), etc., were calculated and discussed on the basis of ion–ion and ion–solvent interactions. These results revealed that the solutions are characterized by ion–solvent interactions rather than by ion–ion interactions and the complex behaves as a long range structure maker. Thermodynamics of viscous flow was discussed in terms of transition state theory.     

Using non-targeted direct analysis in real time-mass spectrometry (DART-MS) to discriminate seeds based on endogenous or exogenous chemicals

Forage seeds are a highly traded agricultural commodity, and therefore, quality control and assurance is high priority. In this study, we have used direct analysis in real time-mass spectrometry (DART-MS) as a tool to discriminate forage seeds based on their non-targeted chemical profiles. In the first experiment, two lots of perennial ryegrass (Lolium perenne L.) seed were discriminated based on exogenous residues of N-(3, 4-dichlorophenyl)-N,N-dimethylurea (Diuron^TM), a herbicide. In a separate experiment, washed and unwashed seeds of the forage legumes white clover (Trifolium repens L.) and alfalfa (Medicago sativa L.) were discriminated based on the presence or absence of oxylipins, a class of endogenous antimicrobial compounds. Unwashed seeds confer toxicity towards symbiotic, nitrogen-fixing rhizobia which are routinely coated on legume seeds before planting, resulting in reduced rhizobial count. This is the first report of automatic introduction of intact seeds in the DART ion source and detecting oxylipins using DART-MS. Apart from providing scope to investigate legume-rhizobia symbiosis further in the context of oxylipins, the results presented here will enable future studies aimed at classification of seeds based on chemicals bound to the seed coat, thereby offering an efficient screening device for industry.