Novosibirsk Institute of Organic Chemistry

Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.

Results of many years’ worth of studies on the determination of carbon, hydrogen, and nitrogen on automated CHNS analyzers were summarized. Catalytic oxide compositions were selected that allow for the analysis of synthetic and natural organic compounds and materials of any elemental composition and structure: polycyclic, condensed aromatic, heterocyclic, carbonaceous (graphites and carbons), organometallic, organoelement, etc.

The design and operational characteristics of the Novosibirsk free electron laser facility are described. Selected experiments in the terahertz range carried out recently at the user stations are surveyed in brief.

Superoxide (O₂ⁱ⁻) has been implicated in the pathogenesis of many human diseases, but detection of the O(2)(•-) radicals in biological systems is limited due to inefficiency of O₂ⁱ⁻ spin trapping and lack of site-specific information. This work studied production of extracellular, intracellular and mitochondrial O₂ⁱ⁻ in neutrophils, cultured endothelial cells and isolated mitochondria using a new set of cationic, anionic and neutral hydroxylamine spin probes with various lipophilicity and cell permeability. Cyclic hydroxylamines rapidly react with O₂ⁱ⁻, producing stable nitroxides and allowing site-specific cO₂ⁱ⁻ detection in intracellular, extracellular and mitochondrial compartments. Negatively charged 1-hydroxy-4-phosphono-oxy-2,2,6,6-tetramethylpiperidine (PP-H) and positively charged 1-hydroxy-2,2,6,6-tetramethylpiperidin-4-yl-trimethylammonium (CAT1-H) detected only extramitochondrial O₂ⁱ⁻. Inhibition of EPR signal by SOD2 over-expression showed that mitochondria targeted mitoTEMPO-H detected intramitochondrial O₂ⁱ⁻ both in isolated mitochondria and intact cells. Both 1-hydroxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine (CP-H) and 1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine (CM-H) detected an increase in cytoplasm O₂ⁱ⁻ stimulated by PMA, but only CM-H and mitoTEMPO-H showed an increase in rotenone-induced mitochondrial O₂ⁱ⁻. These data show that a new set of hydroxylamine spin probes provide unique information about site-specific production of the O₂ⁱ⁻ radical in extracellular or intracellular compartments, cytoplasm or mitochondria.

The chemistry of heterocyclic compounds has traditionally been and remains a bright area of chemical science in Russia. This is due to the fact that many heterocycles find the widest application. These compounds are the key structural fragments of most drugs, plant protection agents. Many natural compounds are also derivatives of heterocycles. At present, more than half of the hundreds of millions of known chemical compounds are heterocycles. This collective review is devoted to the achievements of Russian chemists in this field over the last 15–20 years. The review presents the achievements of leading heterocyclists representing both RAS institutes and university science. It is worth noting the wide scope of the review, both in terms of the geography of author teams, covering the whole of our large country, and in terms of the diversity of research areas. Practically all major types of heterocycles are represented in the review. The special attention is focused on the practical applications of heterocycles in the design of new drugs and biologically active compounds, high-energy molecules, materials for organic electronics and photovoltaics, new ligands for coordination chemistry, and many other rapidly developing areas. These practical advances would not be possible without the development of new fundamental transformations in heterocyclic chemistry.<br> Bibliography — 2237 references.

Abstract Monoterpenes and their derivatives play an important role in the creation of new biologically active compounds including drugs. The review focuses on the data on various types of biological activity exhibited by monoterpenes and their derivatives, including analgesic, anti-inflammatory, anticonvulsant, antidepressant, anti-Alzheimer, anti-Parkinsonian, antiviral, and antibacterial (anti-tuberculosis) effects. Searching for novel potential drugs among monoterpene derivatives shows great promise for treating various pathologies. Special attention is paid to the effect of absolute configuration of monoterpenes and monoterpenoids on their activity.

An amorphous solid dispersion (SD) of curcumin (Cur) with disodium glycyrrhizin (Na2GA) was prepared by mechanical ball milling. Curcumin loaded micelles were self-formed by Na2GA when SD dissolved in water. The physical properties of Cur SD in solid state were characterized by differential scanning calorimetry, X-ray diffraction studies, and scanning electron microscope. The characteristics of the sample solutions were analyzed by reverse phase HPLC, UV–visible spectroscopy, 1H NMR spectroscopy, gel permeation LC, and transmission electron microscopy. In vitro cytotoxic tests demonstrated that Cur SD induced higher cytotoxicity against glioblastoma U-87 MG cells than free Cur. Besides, an improvement of membrane permeability of Cur SD was confirmed by parallel artificial membrane permeability assay. Further pharmacokinetic study of this SD formulation in rat showed a significant ∼19-fold increase of bioavailability as comparing to free Cur. Thus, Cur SD provide a more potent and efficacious formulation for Cur oral delivery.

The effect of nanoparticle size and structure on XRD and SAXS patterns was investigated using modeling with the Debye scattering equation for a series of nanoparticles (NP) with the positions of atoms kept according to the bulk lattice and after structure relaxation. The purpose of research was to determine if the changes in XRD peak positions for NP are entirely due to the well-known effects of lattice parameter change or if additional effects can arise from the size itself. It was found that for very small NPs with sizes below 5 nm, the size itself influences the XRD patterns. This effect can be caused by interference fringes and is not taken into account when considering XRD patterns in standard software. The research demonstrates that new methods for XRD pattern treatment of very small nanoparticles should be developed.

The biological activity of natural and semisynthetic lupane triterpenoids is discussed in a two-part review. The first part is devoted to the pharmacological properties of natural lupane triterpenoids. Betulinic acid has proven to be the most effective antitumor agent among more than fifty natural lupanes.

International audience

SIGNIFICANCE: Oxidative stress contributes to numerous pathophysiological conditions such as development of cancer, neurodegenerative, and cardiovascular diseases. A variety of measurements of oxidative stress markers in biological systems have been developed; however, many of these methods are not specific, can produce artifacts, and do not directly detect the free radicals and reactive oxygen species (ROS) that cause oxidative stress. Electron paramagnetic resonance (EPR) is a unique tool that allows direct measurements of free radical species. Cyclic hydroxylamines are useful and convenient molecular probes that readily react with ROS to produce stable nitroxide radicals, which can be quantitatively measured by EPR. In this work, we critically review recent applications of various cyclic hydroxylamine spin probes in biology to study oxidative stress, their advantages, and the shortcomings. Recent Advances: In the past decade, a number of new cyclic hydroxylamine spin probes have been developed and their successful application for ROS measurement using EPR has been published. These new state-of-the-art methods provide improved selectivity and sensitivity for in vitro and in vivo studies. CRITICAL ISSUES: Although cyclic hydroxylamine spin probes EPR application has been previously described, there has been lack of translation of these new methods into biomedical research, limiting their widespread use. This work summarizes "best practice" in applications of cyclic hydroxylamine spin probes to assist with EPR studies of oxidative stress. FUTURE DIRECTIONS: Additional studies to advance hydroxylamine spin probes from the "basic science" to biomedical applications are needed and could lead to better understanding of pathological conditions associated with oxidative stress. Antioxid. Redox Signal. 28, 1433-1443.

INTRODUCTION: Usnic acid (UA) is a lichen-derived secondary metabolite with a unique dibenzofuran skeleton and is commonly found in lichenized fungi of the genera Usnea and Cladonia. Usnic acid has been incorporated for years in cosmetics, perfumery, and traditional medicines. It has a wide range of bioactivities, including antimicrobial, antiviral, anticancer, anti-inflammatory properties. AREAS COVERED: This review covers patents on therapeutic activities of UA and its synthetic derivatives published during the period 2000-2017. EXPERT OPINION: UA demonstrates excellent anticancer and antimicrobial properties. However, its application was withdrawn due to acute liver toxicity reported with chronic consumption. The broad spectrum of its biological activity indicates high the variability of UA's binding preferences. The main idea to be addressed in the future should include the synthesis of UA derivatives because these might possess increased bioactivity, bioavailability and decreased toxicity. It is noteworthy that UA derivatives possessed better antibacterial, antitubercular, and anticancer activity than the parent compound . Most importantly, UA and its analogs (to a greater extent than UA) can be useful in cancer drug treatment. They have the potential for joint application with other anticancer drugs in order to overcome drug resistance.

In recent years, research dealing with organic paramagnetic compounds such as stable radicals and high-spin systems has been focused on applied aspects. Several key trends have formed in the application and, hence, in the function-oriented synthesis of organic radicals and polyradicals. This review addresses one of such trends in which the dominant role is played by so-called conjugated nitroxides. Their specific feature is the presence of any unsaturated moiety (C=C, C=N or C=O multiple bond; aromatic or heteroaromatic ring; fused polyaromatic system) adjacent to the nitroxide group. The achievements of the chemistry of conjugated nitroxides are presented, and their physicochemical properties, magneto-structural correlations and practical applications are discussed.<br> The bibliography includes 641 references.

The alkylation by ethylnitrosourea of phosphodiester bonds in yeast tRNAPhe, tRNAVal and in Escherichia coli tRNAGlu, tRNAfMet, tRNAmMet and tRNAPhe was investigated under various conditions. In unfolded tRNAs the reactivities of phosphates in various positions toward the reagent were similar. In the folded tRNAs remarkable differences in reactivities of phosphates located in various positions of the molecules were observed. In yeast and E. coli tRNAPhe, reactivities of phosphates in positions 9, 10, 11, 19, 49, 58, 59 and 60 were found to be strongly decreased. Some decrease in reactivity was observed for phosphates 23 and 24. Spermine and ethidium bromide did not influence the pattern of phosphate alkylation in the T psi C arm of yeast tRNAPhe. Our solution results fit with the crystal structure of tRNAPhe with respect to the potential availability of the phosphates in this tRNA to solvent as shown by others. Judging from the pattern of phosphate reactivities, the structure of E. coli tRNAPhe is very similar to that of yeast tRNAPhe. Upon thermal denaturation of the yeast tRNAPhe, the reactivity of the low-reactive phosphates increased, demonstrating a cooperative melting curve. A comparison of the patterns of phosphate alkylation in several tRNAs, essentially in their T psi C arms, revealed a striking similarity, suggesting that the folding of these tRNAs is essentially similar.

Metal–organic frameworks (MOFs) are the promising nanomaterials for separation of molecules with close dimensions and structures, such as various types of isomers. The efficiency of separation can be greatly enhanced if the apertures of the nanosized windows, controlling the diffusion of a particular molecule inside the cavities, are fine-tuned by external stimuli. We report the new approach for precise measurement of window sizes in ZIF-8 MOF and employ it in efficient separation of xylenes, which is of high practical importance. For this sake, we synthesized ZIF-8 with embedded stable nitroxides in the pores and applied electron paramagnetic resonance spectroscopy for in situ kinetic measurement of the diffusion of various guest molecules through the material. Slight variation of temperature within 298–333 K allowed tuning of the windows and reaching optimum conditions for separation of p-, m-, and o-xylenes with the efficiency up to 92–95%. The developed methodology provides deeper understanding of steric and kinetic aspects of molecular diffusion in ZIF-8 and paves the way to rational optimization of other MOF-based separation applications.

It has been previously suggested that overexpression of mitochondrial superoxide dismutase (SOD) attenuates cancer development; however, the exact mechanism remains unclear. In this work, we have studied the direct effect of the mitochondria-targeted superoxide scavenger, (2-(2,2,6,6-tetramethylpiperidin-1-oxyl-4-ylamino)-2-oxoethyl)triphenylphosphonium chloride (mitoTEMPO), on B16-F0 mouse melanoma cells and tumor growth in a nude mouse model of human melanoma. We show that scavenging of mitochondrial superoxide inhibited cell growth, reduced viability, and induced apoptosis in melanoma cells, but did not affect nonmalignant skin fibroblasts. Diminished mitochondrial superoxide inhibited redox-dependent Akt, restored activity of mitochondrial pyruvate dehydrogenase, and reduced HIF1-α and lactate dehydrogenase expression in cancer cells. Suppression of glycolysis in mitoTEMPO-treated melanoma cells resulted in a significant drop of cellular adenosine-5'-triphosphate and induced cell death. In vivo mitoTEMPO treatment effectively suppressed growth of established tumor in the mouse model of human melanoma. Therefore, our data lead to the hypothesis that scavenging of mitochondrial superoxide selectively inhibits redox-sensitive survival and metabolic pathways, resulting in cancer cell death. In contrast to existing anticancer therapies, inhibition of mitochondrial superoxide may represent a novel specific anticancer treatment with reduced cytotoxic side effects.

Camphor based heterocyclic systems containing 1,3-thiazolidin-4-one and thiazole rings showed promising antiviral activity towards Orthopoxviruses .

Abstract Two novel rhenium cluster compounds, K 4 [Re 6 S 8 (OH) 6 ] · 8H 2 O ( 1 ) and K 4 [Re 6 Se 8 (OH) 6 ] · 8H 2 O ( 2 ), containing octahedral cluster chalcogenide anionic complexes [Re 6 Q 8 (OH) 6 ] 4– with terminal hydroxo ligands have been synthesized by the reaction of Re 6 Q 8 Br 2 (Q = S, Se) with molten KOH. Two chalcohalide compounds, one known (Cs 4 [Re 6 S 8 Br 6 ] · 2H 2 O, 3 ) and another new (Cs 3 [Re 6 Se 8 Cl 6 ] · 2H 2 O, 4 ), were prepared by reactions of 1 and 2 with CsX and HX (X = Br, Cl) in an aqueous solution. Compounds 1 , 2 , and 4 have been characterized by the single‐crystal X‐ray diffraction method. Compounds 1 and 2 are crystallized in triclinic space group P $\bar {1}$ with one formula unit in the cell of dimensions a = 8.4936(8) Å, b = 8.9101(11) Å, c = 10.5940(13) Å, α = 77.935(11)°, β = 75.933(9)°, γ = 71.244(10)°, V = 728.9(1) Å 3 (compound 1 ) and a = 8.613(1) Å, b = 8.996(1) Å, c = 10.057(1) Å, α = 78.587(2)°, β = 77.811(2)°, γ = 71.728(2)°, V = 715.9(2) Å 3 (compound 2 ). Compound 4 crystallizes in the monoclinic space group P 2 1 / n with two formula units in the cell of dimensions a = 9.819(3) Å, b = 12.925(4) Å, c = 11.756(4) Å, β = 113.38(3)°, V = 1369.6(8) Å 3 . Compounds 1 and 2 display luminescent properties. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

The orchestrated interaction of transmembrane proteins with other molecules mediates several crucial biological processes. Detergent solubilization may significantly alter or even abolish such hetero-oligomeric interactions, which makes observing them at high resolution in their native environment technically challenging. Dipolar electron paramagnetic resonance (EPR) techniques such as pulsed electro-electron double resonance (PELDOR) can provide very precise distances within biomolecules. To concurrently determine the inter-subunit interaction and the intra-subunit conformational changes in hetero-oligomeric complexes, a combination of different spin labels is required. Orthogonal spin labeling using a triarylmethyl (TAM) label in combination with a nitroxide label is used to detect protein-ligand interactions in native lipid bilayers. This approach provides a higher sensitivity and total selectivity and will greatly facilitate the investigation of multimeric transmembrane complexes employing different spin labels in the native lipid environment.

Approach for in vivo real-time assessment of tumor tissue extracellular pH (pH(e)), redox, and intracellular glutathione based on L-band EPR spectroscopy using dual function pH and redox nitroxide probe and disulfide nitroxide biradical, is described. These parameters were monitored in PyMT mice bearing breast cancer tumors during treatment with granulocyte macrophage colony-stimulating factor. It was observed that tumor pH(e) is about 0.4 pH units lower than that in normal mammary gland tissue. Treatment with granulocyte macrophage colony-stimulating factor decreased the value of pH(e) by 0.3 units compared with PBS control treatment. Tumor tissue reducing capacity and intracellular glutathione were elevated compared with normal mammary gland tissue. Granulocyte macrophage colony-stimulating factor treatment resulted in a decrease of the tumor tissue reducing capacity and intracellular glutathione content. In addition to spectroscopic studies, pH(e) mapping was performed using recently proposed variable frequency proton-electron double-resonance imaging. The pH mapping superimposed with MRI image supports probe localization in mammary gland/tumor tissue, shows high heterogeneity of tumor tissue pH(e) and a difference of about 0.4 pH units between average pH(e) values in tumor and normal mammary gland. In summary, the developed multifunctional approach allows for in vivo, noninvasive pH(e), extracellular redox, and intracellular glutathione content monitoring during investigation of various therapeutic strategies for solid tumors.