На сайте журнала Applied Sciences,  (IF 2,217I) опубликована статья с участием сотрудников Института  - Е.С. Можайцева,  А..А. Мункуева, Е.В. Суслова ,  Д.В. Корчагиной,  К.П. Волчо и  Н.Ф. Салахутдинова

Редакция журнала обозначила статью "Избранное"

Featur Paper

The Development of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Combination of Monoterpene and Adamantine Moieties via Amide or Thioamide Bridges

Abstract

Eleven amide and thioamide derivatives with monoterpene and adamantine substituents were synthesised. They were tested for their activity against the tyrosyl-DNA phosphodiesterase 1 DNA (Tdp1) repair enzyme with the most potent compound , having an IC₅₀ value of 0.64 µM. When tested in the A-549 lung adenocarcinoma cell line, no or very limited cytotoxic effect was observed for the ligands. However, in conjunction with topotecan, a well-established Topoisomerase 1 (Top1) poison in clinical use against cancer, derivative 46a was very cytotoxic at 5 µM concentration, displaying strong synergism. This effect was only seen for 46a (IC₅₀—3.3 µM) albeit some other ligands had better IC₅₀ values. Molecular modelling into the catalytic site of Tdp1 predicted plausible binding mode of 46a, effectively blocking access to the catalytic site. Full article

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В журнале Angewandte Chemie Int. Ed.,  (IF 12,257I) опубликована статья с участием сотрудников Института  - к.х.н. Л.В. Политанской , к.х.н. Ю.Ф. Полиенко, д.х.н. Е.В. Третьякова, к.х.н. О.Ю. Рогожниковой,  к.х.н. Д.В. Трухина, к.х.н. В.М. Тормышева, д.х.н. Е. Г. Багрянской:

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR

Abstract

Precise nanoscale distance measurements by pulsed Electron Paramagnetic Resonance (EPR) play crucial role in structural studies of biomolecules and their complexes. The properties of spin labels used in this approach are of paramount importance, since they determine the sensitivity limits, attainable distances and proximity to biological conditions, including physiological temperatures. Herewith, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements. Hyperpolarization and narrower spectrum of fullerenes compared to other triplets (e.g., porphyrins) boost the sensitivity, and superior relaxation properties allow PD EPR measurements up to a near‐room temperature. The capabilities of new approach are demonstrated using fullerene‐nitroxide and fullerene‐triarylmethyl pairs, as well as supramolecular complex of fullerene with nitroxide‐labeled protein. Therefore, photoexcited triplet fullerenes can be considered as new spin labels with the outstanding spectroscopic properties for future structural studies of biomolecules. 

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В  журнале Nucleic Acids Research (IF 11,147I) опубликована статья с участием сотрудников Института  - О.А. Крумкачева, А. А. Кужелев,  В.М. Тормышев, Ю.Ф. Полиенко, Е. Г. Багрянская:

DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

Abstract

A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5′ ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1. 

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В  журнале Biomolecules,  (IF 4,964I) опубликована статья с участием сотрудников Института: д.х.н. Е. Шульц и Т. Рыбаловой:  

Chelidonic Acid and Its Derivatives from Saussurea Controversa: Isolation, Structural Elucidation and Influence on the Osteogenic Differentiation of Multipotent Mesenchymal Stromal Cells In Vitro

Abstract

4-oxo-4H-pyran-2.6-dicarboxylic acid (chelidonic acid, ChA) in the native state and in the complex with calcium [Ca(ChA)(H₂O)₃], named saucalchelin (CaChA), was isolated from the extract of Saussurea controversa leaves for the first time for the Asteraceae family. The structure of ChA was determined by NMR, MS and confirmed by X-ray analysis of its monomethyl ester, and CaChA was described by IR, ICP-MS, CHN analysis. The yield of ChA and CaChA was 45 mg/g and 70 mg/g of extract, respectively. The osteogenic activity of ChA, n-monobutyl ester of chelidonic acid, and CaChA has been studied in vitro in a 21-day culture of human adipose-derived multipotent mesenchymal stromal cells (hAMMSCs) in a standard nutrient medium without osteogenic supplements. CaChA significantly stimulated the growth of cell mass and differentiation of hAMMSCs into osteoblasts with subsequent mineralization of the culture and it may be a promising substance for accelerating bone tissue regeneration and engineering. View Full-Text

Keywords: Saussurea controversa DC (Asteraceae); chelidonic acid; 4-oxo-4H-pyran-2.6-dicarboxylic acid esters; X-ray diffraction analysis; human multipotent mesenchymal stromal cells

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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В  журнале Journal of Catalysis,  (IF 6,759I) опубликована статья с участием сотрудников Института  - г.н.с. ЛФАВ, д.х.н., проф. РАН К.П. Волчо и зав. ЛФАВ, д.х.н., проф. Н.Ф. Салахутдинова:

Highly selective Prins reaction over acid-modified halloysite nanotubes for synthesis of isopulegol-derived 2H-chromene compound.

Abstract

Prins reaction of terpenoid (−)-isopulegol with thiophene-2-carbaldehyde giving in substituted octahydro-2H-chromen-4-ol (as 4R- and 4S-diastereomers) was studied for the first time over a series of halloysite nanotubes (Dragon Mine, USA), treated with 1–30% HCl. Materials have been characterized by MAS NMR, XRD, XRF, N2adsorption, FTIR with pyridine, SEM, TEM and thermal analysis methods. The quantitative data on the effect of acid treatment conditions on the content of structural units of halloysite are presented for the first time. The effect HNT treatment conditions, reaction temperature, catalyst loading, initial concentration of substrates on overall selectivity and 4R/4S ratio was studied. The diastereomers ratio decreased from 6.5 for air-dry nanotubes to 3.6 for counterparts dried at 350 °C, which clearly indicates formation of 4R-isomer on weak Brønsted acid sites At 99% isopulegol conversion in cyclohexane over HNT treated with 5% HCl an unprecedented selectivity towards 4R alone (ca.80%) was achieved close to the sum of both diastereomers on a commercial montmorillonite K-10. The 4R/4S ratio decreased with an increase in the concentration of acid sites. The excellent selectivity on halloysite was due to the predominance of weak acid sites. On the contrary, a low chromenols yield (ca. 30%) was observed over strong Brønsted acid (resin Amberlyst-15) related to direct formation of dehydration products from the substrates. Kinetic modelling shows a substantial difference in the order to the catalyst for the dried at 110 °C resin (1.1 ± 0.12) and air-dry halloysite (1.95 ± 0.09) for the target 4R-isomer formation, which clearly indicates the key role of water in the reaction. Based on experimental results and kinetic modelling a dual mechanism of halloysite action was proposed implying formation of an intermediate with the reagents and transfer of the surface water to the intermediate giving chromenols. Stability of the catalytic properties and reusability of HNT were demonstrated. Thus, modified halloysite nanotubes can be considered as a novel type of highly selective catalysts for the Prins reaction.

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На сайте журнала The Journal of Organic Chemistry,  (IF 4,805I) опубликована статья с участием сотрудников Института  - А.М. Генаева, Л.Н. Щеголевой, Г.Е. Сальникова, А.В. Шернюкова,  Л.А. Шундрина, И.К. Шундриной:

Acid-Catalyzed Versus Thermally Induced C1–C1′ Bond Cleavage in 1,1′-Bi-2-naphthol: An Experimental and Theoretical Study

Abstract

Experiments show that 1,1′-bi-2-naphthol (BINOL) undergoes facile C1–C1′ bond cleavage under action of triflic acid at temperatures above 0 °C to give mainly 2-naphthol along with oligomeric material. CASSCF and MRMP//CASSCF computations have demonstrated unambiguously that this unusual mode of scission of the biaryl bond can occur in the C1,C1′-diprotonated form of BINOL via a mechanism involving homolytic cleavage prompted by the intramolecular electrostatic repulsion. These findings also provide insights into the mechanism of a comparatively easy thermal cleavage of BINOL, implying the intermediacy of its neutral diketo form. 

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На сайте журнала CrystEngComm  (IF 3,304) опубликована статья с участием сотрудников Института  А.С. Виноградова, В.М. Карпова, В.Е. Платонова,

Structural diversity of zinc(II) coordination polymers with octafluorobiphenyl-4,4′-dicarboxylate based on mononuclear, paddle wheel and cuboidal units

Abstract

We present a series of six novel Zn(II) complexes containing anions of perfluorinated biphenyl-4,4′-dicarboxylate (oFBPDCБ²⁻). Among them are the 0D complex [Zn(eg)₃](oFBPDC) (eg =

ethylene glycol), the 1D [Zn(H₂O)(ur)(oFBPDC)] (ur = urotropine) and [Zn(CH₃OH)₂(CH₃OCH₂CH₂OH)(oFBPDC)] and the 2D layered [Zn₂(CH₃CN)₂(oFBPDC)₂]·2C₆H₆·2CH₃CN,

[Zn₂(H₂O)₂(oFBPDC)₂]·4(CH₃)₂CO, [{Zn₄(μ₃-OCH₃)₄}(CH₃OH)₄(oFBPDC)₂]·[{Zn₄(μ₃-OCH₃)₄}(H₂O)(CH₃OH)₃(oFBPDC)₂]·13CH₃OH. The latter coordination polymer is built up by

unique Zn₄(OCH₃)₄ cuboidal units. The complexes are characterized by single-crystal X-ray diffraction, FT-IR, elemental analysis, and TGA. Investigation of the CO₂ adsorption at 195 K on

[Zn₂(CH₃CN)₂(oFBPDC)₂] and [Zn₂(H₂O)₂(oFBPDC)₂] of the layered polymeric structure revealed that they have BET surface areas of 334.8 and 150.6 m² g⁻¹, respectively. 

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В журнале Materials, 2019, V. 12, N 5, Pp. 688-707  (IF 2,467) опубликован обзор с участием сотрудников Института  Mariya Edeleva, Elena Bagryanskaya

Smart Control of Nitroxide-Mediated Polymerization Initiators’ Reactivity by pH, Complexation with Metals, and Chemical Transformations

Abstract

Because alkoxyamines are employed in a number of important applications, such as nitroxide-mediated polymerization, radical chemistry, redox chemistry, and catalysis, research into their reactivity is especially important. Typically, the rate of alkoxyamine homolysis is strongly dependent on temperature. Nonetheless, thermal regulation of such reactions is not always optimal. This review describes various ways to reversibly change the rate of C–ON bond homolysis of alkoxyamines at constant temperature. The major methods influencing C–ON bond homolysis without alteration of temperature are protonation of functional groups in an alkoxyamine, formation of metal–alkoxyamine complexes, and chemical transformation of alkoxyamines. Depending on the structure of an alkoxyamine, these approaches can have a significant effect on the homolysis rate constant, by a factor of up to 30, and can shorten the half-lifetime from days to seconds. These methods open new prospects for the application of alkoxyamines in biology and increase the safety of (and control over) the nitroxide-mediated polymerization method. View Full-Text

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В журнале  Успехи химии/Russian Chemical Reviews  (IF 3.991) опубликован обзор сотрудников Института

Г.И. Бородкина и В.Г. Шубина

Прогресс и перспективы использования фотокатализа в синтезе фторорганических соединений

Progress and prospects in the use of photocatalysis for the synthesis of organofluorine compounds

Анотация

Обобщены и проанализированы данные по синтезу фторированных органических соединений с использованием фотокатализа. Особое внимание уделено рассмотрению механизмов фотокаталитических реакций и проблеме селективности.
Библиография — 173 ссылки.

Abstract

Data on the synthesis of fluorinated organic compounds by photocatalysis are systematically considered and analyzed. The attention is focused on the mechanisms of photocatalytic reactions and the selectivity problem.
The bibliography includes 173 references.

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Showcasing collaborative research from Rijksuniversiteit Groningen in The Netherlands, Lomonosov Moscow State University, Novosibirsk State University and Vorozhtsov Novosibirsk Institute of Organic Chemistry, Russia Long-range exciton transport in brightly fluorescent furan/phenylene co-oligomer crystals Design of materials combining bright luminescence and charge transport is one of the strategic challenges in organic optoelectronics. Extremely light doping of organic crystals with highly fluorescent molecules enhances the luminescence provided the exciton diffusion length is long enough to reach the dopant and have the exciton energy transferred to the dopant. We present a comprehensive study of singlet exciton diffusion in a brightly luminescent doped semiconductor crystal. The high potential of this material is demonstrated by fabricating solution-processed organic light-emitting transistors. As featured in: ISSN 2050-7526 REVIEW ARTICLE Jihyun Kim et al. Radiation damage effects in Ga 2 O 3 materials and devices Journal of Materials Chemistry C Materials for optical, magnetic and electronic devices rsc.li/materials-c Volume 7 Number 1 7 January 2019 Pages 1–190 rsc.li/materials-c Registered charity number: 207890 See Maxim S. Kazantsev, Dmitry Yu. Paraschuk, Maxim S. Pshenichnikov et al., J. Mater. Chem. C, 2019,

First published: 22 October 2018

Volume 130, January 2019, Pages 581-593


 https://doi.org/10.1039/C8TC04151B

Abstract

The design of light-emitting crystalline organic semiconductors for optoelectronic applications requires a thorough understanding of the singlet exciton transport process. In this study, we show that the singlet exciton diffusion length in a promising semiconductor crystal based on furan/phenylene co-oligomers is 24 nm. To achieve this, we employed the photoluminescence quenching technique using a specially synthesized quencher, which is a long furan/phenylene co-oligomer that was facilely implanted into the host crystal lattice. Extensive Monte-Carlo simulations, exciton–exciton annihilation experiments and numerical modelling fully supported our findings. We further demonstrated the high potential of the furan/phenylene co-oligomer crystals for light-emitting applications by fabricating solution-processed organic light emitting transistors.

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В журнале European Journal of Medicinal Chemistry Volume 161, 1 January 2019, Pages 581-593  (IF=4,816) опубликована статья с участием сотрудников Института:

О.А. Лузиной, Д.Н. Соколова, К.П. Волчо, Н.Ф.Салахутдинова

Novel tyrosyl-DNA phosphodiesterase 1 inhibitors enhance the therapeutic impact of topoteсan on in vivo tumor models

First published: 05 October 2018

Volume 130, January 2019, Pages 581-593


 https://doi.org/10.1016/j.ejmech.2018.10.055

Abstract

The druggability of the tyrosyl-DNA phosphodiesterase 1 (Tdp1) enzyme was investigated in conjunction with topoisomerase 1 inhibition. A novel class of thiazole, aminothiazole and hydrazonothiazole usnic acid derivatives was synthesized and evaluated as Tdp1 inhibitors and their ability to sensitize tumors to topotecan, a topoisomerase inhibitor in clinical use. Of all the compounds tested, four hydrazinothiazole derivatives,  20c, 20d, 20h and 20i, inhibited the enzyme in the nanomolar range. The activity of the compounds was verified by affinity experiments as well as supported by molecular modelling. The most effective Tdp1 inhibitor, 20d, was ton-toxic and increased the effect of topotecan both in vitro and in vivo in the Lewis lung carcinoma model. Furthermore, 20d showed significant increase in the antitumor and antimetastatic effect of topotecan in mice. The results presented here justify compound 20d to be considered as a drug lead for antitumor therapy.

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В журнале Free Radical Biology and Medicine (IF=6,02) опубликована статья с участием сотрудников Института О.Ю. Рогожниковой, Д. В. Трухина, В.М. Тормышева

A radical containing injectable in-situ-oleogel and emulgel for prolonged in-vivo oxygen measurements with CW EPR

Abstract

Molecular oxygen, reactive oxygen species and free radicals derived from oxygen play important roles in a broad spectrum of physiological and pathological processes. The quantitative measurement of molecular oxygen in tissues by electron paramagnetic resonance (EPR) has great potential for understanding and diagnosing a number of diseases, and for developing and guiding therapies. This requires improvements in the free radical probe systems that sense and report molecular oxygen levels in vivo. We report on the encapsulation of existing free radical probes in lipophilic gel implants: an in-situ-oleogel and an emulgel, based only on well-known, safe excipients for the incorporation of lipophilic and hydrophilic radicals, respectively. The EPR signals of encapsulated radicals were not altered compared to dissolved radicals. The high solubility of oxygen in lipophilic solvents enhanced oxygen sensitivity. The gels extended the lifetime of the radicals in tissues from tens of minutes to many days, simplifying studies with extended series of measurements. The encapsulated radicals showed a good in vivo response to changes in oxygen supply and seem to circumvent concerns from toxicity of the radical probes. These gels simplify the development of new oxygen-sensitive free radical probes for EPR oximetry by making their in vivo stability, persistence and toxicity a function of the encapsulating gel and not a set of additional requirements for the free radical probe.

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