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На сайте журнала Nucleic Acids Research (IF 11,147I) опубликована статья с участием сотрудников Института :
Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
Alexey A Malygin, Olesya A Krumkacheva, Dmitri M Graifer, Ivan O Timofeev, Anastasia S Ochkasova, Maria I Meschaninova, Alya G Venyaminova, Matvey V Fedin, Michael Bowman, Galina G Karpova, Elena G Bagryanskayaa
Nucleic Acids Research, Volume 47, Issue 22, 16 December 2019, Pages 11850–11860 First published: 14 Nov 2019
The features of previously unexplored labile complexes of human 40S ribosomal subunits with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of RNAs to the ribosomal protein uS3 through its peptide 55–64 located outside the mRNA channel, were studied by EPR spectroscopy methods. Analysis of subatomic 40S subunit models showed that a likely site for labile RNA binding is a cluster of positively charged amino acid residues between the mRNA entry site and uS3 peptide 55–64. This is consistent with our finding that the 3′-terminal mRNA fragment hanging outside the 40S subunit prevents the cross-linking of an RNA derivative to this peptide. To detect labile complexes of 40S subunits with RNA by DEER/PELDOR spectroscopy, an undecaribonucleotide derivative with nitroxide spin labels at terminal nucleotides was utilized. We demonstrated that the 40S subunit channel occupancy with mRNA does not affect the RNA derivative binding and that uS3 peptide 55–64 is not involved in binding interactions. Replacing the RNA derivative with a DNA one revealed the importance of ribose 2′-OH groups for the complex formation. Using the single-label RNA derivatives, the distance between the mRNA entry site and the loosely bound RNA site on the 40S subunit was estimated.
В журнале ACS Chemical Neuroscience (IF 3,861) опубликована статья с участием сотрудников Института: к.х.н.О.В. Ардашова (снс ЛФАВ), к.б.н. А.В. Павловой (нс ЛФИ), к.б.н. Е.А. Морозовой (снс ЛФИ) , к.х.н. Д.В. Корчагиной (нс ГЯМР), Г.Е. Сальникова (снс, ГЯМР), к.х.н. А.М. Генаева (снс ЛМР), к.х.н. О.С. Патрушевой (нс ЛФАВ), Н. С. Ли-Жуланова (мнс ЛНТПС), д.б.н. Т.Г. Толстиковой (завлаб ЛФИ), д.х.н. К.П. Волчо (гнс ЛФАВ), д.х.н. Н.Ф. Салахутдинова (зав отделм ОМХ)
A Novel Small Molecule Supports the Survival of Cultured Dopamine Neurons and May Restore the Dopaminergic Innervation of the Brain in the MPTP Mouse Model of Parkinson’s Disease
Oleg V. Ardashov, Alla V. Pavlova, Arun Kumar Mahato, Yulia Sidorova, Ekaterina A. Morozova, Dina V. Korchagina, Georgi E. Salnikov, Alexander M. Genaev, Oksana S. Patrusheva, Nikolay S. Li-Zhulanov, Tat’yana G. Tolstikova, Konstantin P. Volcho, Nariman F. Salakhutdinov
ACS Chemical Neuroscience, 2019, 10, 10, 4337-4349
We previously showed that monoterpenoid (1R,2R,6S)-3-methyl-6-(prop-1-en-2-yl)cyclohex-3-ene-1,2-diol 1 alleviates motor manifestations of Parkinson’s disease in animal models. In the present study, we designed and synthesized monoepoxides of (1R,2R,6S)-3-methyl-6-(prop-1-en-2-yl)cyclohex-3-ene-1,2-diol 1 and evaluated their biological activity in the MPTP mouse model of Parkinson’s disease. We also assessed the ability of these compounds to penetrate the blood–brain barrier (BBB). According to these data, we chose epoxide 4, which potently restored the locomotor activity in MPTP-treated mice and efficiently penetrated the BBB, to further explore its potential mechanism of action. Epoxide 4 was found to robustly promote the survival of cultured dopamine neurons, protect dopamine neurons against toxin-induced degeneration, and trigger the mitogen-activated protein kinase (MAPK) signaling cascade in cells of neuronal origin. Meanwhile, neither the survival-promoting effect nor MAPK activation was observed in non-neuronal cells treated with epoxide 4. In the MPTP mouse model of Parkinson’s disease, compound 4 increased the density of dopamine neuron fibers in the striatum, which can highlight its potential to stimulate striatal reinnervation and thus halt disease progression. Taken together, these data indicate that epoxide 4 can be a promising compound for further development, not only as a symptomatic but also as a neuroprotective and neurorestorative drug for Parkinson’s disease.
На сайте журнала Journal of Catalysis, 2019, Volume 380, December 2019, Pages 145-152 (IF 7,723) опубликована статья с участием сотрудников Института: к.х.н. И.В. Ильиной (снс, ЛФАВ),к.х.н. Д.В. Корчагиной (снс ГЯМР), д.х.н. Ю.В. Гатилова (внс , ГРСА), д.х.н., проф. РАН К.П. Волчо (гнс ЛФАВ), д.х.н., проф. Н.Ф. Салахутдинова (зав.отделом медицинской химии)
Clay nanotubes catalyzed solvent-free synthesis of octahydro-2H-chromenols with pharmaceutical potential from (-)-isopulegol and ketones
Natural halloysite nanotubes (HNT) pretreated with hydrochloric acid were applied for the first time for selective synthesis of octahydro-2H-chromenols (as 4R- and 4S-diastereomers) using terpenoid (-)-isopulegol and ketones as reactants. The main attention was paid to the reaction with acetone, because the resulting 4R-isomer displays antiviral activity. While the drawback of the isopulegol Prins reaction with ketones is a low yield of chromenols, considerably higher values could be achieved using a halloysite catalyst under solvent-free conditions and low temperature (30 °C) giving up to 77% overall selectivity towards chromenols. The isolated yield of the acetone-derived 4R-isomer was 66%, significantly exceeding previous results. The proposed mechanism of isopulegol condensation with ketones is more complex than in the case of aldehydes. Formation of the target chromenols occurs through addition of water to the cyclic intermediate. In parallel interactions of this intermediate with isopulegol lead to stereoselective formation of an ester with the chromene structure, which after hydrolysis gives chromenols. Formation of the ether is opposite to the Prins reaction of aliphatic alcohols with carbonyl compounds, where non-cyclic acetals are typically formed. This clearly confirms that in the Prins reaction of isopulegol with carbonyl compounds, the cyclic intermediate plays a key role. A decrease in the halloysite hydration led to an increase in ether selectivity, while with the increase in the studied catalysts acidity, formation of dehydration by-products increased. A reaction scheme for the products formation was proposed and evaluated by kinetic modelling. A possibility of the catalyst reuse has been also shown. Halloysite nanotubes can be considered as highly selective, eco-friendly, low-cost and reusable catalysts for synthesis of heterocycles based on terpenoids and ketones.
На сайте журнала The Journal of Physical Chemistry C, 2019, 123, 46, 28058-28065 (IF 4,309) опубликована статья с участием сотрудницы Института: д.х.н. Л.В. Щеголевой (внс, ЛЭАСМ)
Magnetic Resonance Characteristics of Negative Polarons in Neat Poly(3-hexyl-thiophene)
Magnetic resonance characteristics of carriers of both electron spin and electric charge (polarons) in conjugated polymers are required for a deeper understanding of properties of these semiconducting materials. In poly(3-hexyl-thiophene), P3HT, which is an important material for photovoltaic applications, such information is available only for positive polarons, which are readily generated in the presence of electron acceptors via photoinduced processes. Influence of an external magnetic field on X-ray-induced delayed fluorescence from undoped P3HT and its solutions allowed us to visualize the spin interactions in the primary polaron pairs and to estimate the g-tensor components (g⊥≈ 2.0023, g|| ≈ 2.008) for the negative charge carriers in P3HT molecules. There is evidence that in neat regioregular P3HT the g-tensor anisotropy for the polarons, migrating along polymer chains, is averaged partially due to irregularities in the polymer structure.
В журнале CrystEngComm, 2019, V. 21, N 39, Pp 5931-5946 (IF 3,382) опубликована статья с участием сотрудников Института к.х.н. Т.А. Вагановой (снс ЛГетС), д.х.н. Ю.В. Гатилова (внс, руководитель группы ГРСА), к.х.н. И.П. Чуйкова (нс ЛМР) и д.х.н. Е.В. Малыхина (гнс ЛГетС)
Impact of molecular packing rearrangement on solid-state fluorescence: polyhalogenated N-hetarylamines vs. their co-crystals with 18-crown-6
Tamara A. Vaganova, Yurij V. Gatilov, Enrico Benassi, Igor P. Chuikov, Denis P. Pishchur and Evgenij V. Malykhin
A series of polyhalogenated hetarylamines and their co-crystals with 18-crown-6 ether was used to reveal the effect of co-crystallization on the supramolecular structure and fluorescence properties as well as the relationship between these characteristics and peculiarities of the hetarylamine chemical structure (α- or γ-position of the NH2 group, number of Cl and F substituents, pyridine or quinoline framework, presence of a fluorophore fragment). Incorporation of crown ether into the crystal matrix of the hetarylamine results in a significant rearrangement of the supramolecular structure. In all cases, the N–H⋯Nhet and N–H⋯F H-bonds are replaced by the N–H⋯Ocrown bond. Changes in π-electron interactions that affect fluorescence characteristics depend on the amine structure. In the co-crystals of γ-aminopyridines, replacement of C–F⋯πF interactions with πF⋯πF stacking causes the fluorescence quenching or a bathochromic shift of λem, whereas replacement of πF⋯πF or πF⋯πH stacking with C–F⋯πF interactions or πH⋯πH stacking in the co-crystals of α-aminopyridines is accompanied by the hypsochromic shift of λem. γ-Aminopyridines show more pronounced changes in fluorescence characteristics as compared to α-aminopyridines, the effect being dependent on the nature of the halogen substituents. The fluorescence properties of aminoquinolines, regardless of the amino group location, are insignificantly modified due to the ability of the extended π-system to minimize interaction changes. Exploration of the nature of the excited states of isolated molecules, homocrystals and co-crystals using quantum mechanical calculations evidences that fluorescence quenching occurs due to EET, facilitated by the presence of crown ether molecules. The bathochromic and hypsochromic shifts of emission are caused by the change in a mutual orientation of the hetarylamine molecules with subsequent different stabilization of the ground and excited states. Using DSC, the co-crystals' supramolecular structure was found to self-organize from solution or melt and to regenerate in the melting–crystallization cycle. The revealed modification of the hetarylamines' fluorescence properties due to the formation of co-crystals with crown ether seems to be promising for use in solid-state supramolecular chemo and thermo sensors (indicators).
На сайте журнала Journal of Natural Products, (IF 4,257I) опубликована статья с участием сотрудников Института - К.С. Ковалёвой (мнс ЛНПТС), д.х.н. О.И. Яровой (внс ЛФАВ) и д.х.н., проф. Н.Ф. Салахутдинова (зав. отделом медицинской химии)
Dehydroabietylamine Ureas and Thioureas as Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Enhance the Antitumor Effect of Temozolomide on Glioblastoma Cells
Kseniya Kovaleva, Olga Oleshko, Evgeniya Mamontova, Olga Yarovaya, Olga Zakharova, Alexandra Zakharenko, Alena Kononova, Nadezhda Dyrkheeva, Sergey Cheresiz, Andrey Pokrovsky, Olga Lavrik, Nariman Salakhutdinov
Journal of Natural Products, 2019, V. 82, N 9, Pp 2443-2450
A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors was found among resin acid derivatives. Several novel ureas and thioureas derived from dehydroabietylamine were synthesized and tested for TDP1 inhibition. The synthesized compounds showed IC50 values in the range of 0.1 to 3.7 μM and demonstrated low cytotoxicity against the human tumor cell lines U-937, U-87MG, MDA-MB, SK-Mel8, A-549, MCF7, T98G, and SNB19. Several compounds showed enhancement of the cytotoxic activity of the alkylating agent temozolomide, which is used as a first line therapy against glioblastoma (GBM), in the GBM cell lines U-87MG and SNB19.
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
Arina A. Chepanova, Evgenii S. Mozhaitsev, Aldar A. Munkuev, Evgeniy V. Suslov, Dina V. Korchagina, Olga D. Zakharova, Alexandra L. Zakharenko, Jinal Patel, Daniel M. Ayine-Tora, Jóhannes Reynisson, Ivanhoe K. H. Leung, Konstantin P. Volcho, Nariman F. Salakhutdinov and Olga I. Lavrik
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
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
Olesya A. Krumkacheva, Ivan O. Timofeev, Larisa V. Politanskaya, Yuliya F. Polienko, Evgeny V. Tretyakov, Olga Yu. Rogozhnikova, Dmitry V. Trukhin, Victor M. Tormyshev, Alexey S. Chubarov, Elena G. Bagryanskaya, Matvey V. Fedin
Angewandte Chemie, 2019, V. 131, N 38, Pp 13405-13409
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.
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
Olesya A Krumkacheva, Georgiy Yu Shevelev, Alexander A Lomzov, Nadezhda S Dyrkheeva, Andrey A Kuzhelev, Vladimir V Koval, Victor M Tormyshev, Yuliya F Polienko, Matvey V Fedin, Dmitrii V Pyshnyi, Olga I Lavrik, Elena G Bagryanskaya
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.
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
El. Avdeeva, E. Shults, T. Rybalova, Ya. Reshetov, E. Porokhova, I. Sukhodolo, L. Litvinova, V. Shupletsova, O. Khaziakhmatova, I. Khlusov, A. Guryev, M. Belousov
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
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).
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.
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.
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
Alexander M. Genaev, Lyudmila N. Shchegoleva, George E. Salnikov, Andrey V. Shernyukov, Leonid A. Shundrin, Inna K. Shundrina, Zhongwei Zhu, Konstantin Yu. Koltunov
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.
