?
Docking and Molecular Dynamics Studies on DNA-Heterocyclic Enediynes Interaction to Identify the Preferred Binding Mode
Russian Journal of General Chemistry. 2024. Vol. 94. No. 1. P. S100–S119.
Enediyne antibiotics are a class of potent DNA-cleaving antitumor agents. Searching for promising analogs of enediyne antibiotics, the features of interaction with the DNA of enediynes fused with heterocycles have been studied using molecular modeling methods. Depending on their structure, 10-membered heteroenediynes can exhibit both intercalator properties and bind to the minor groove of DNA. Variation of the heterocyclic part annulated with the enediyne cycle as well as the attachment of substituents at the enediyne core makes it possible to change the DNA method of binding mode, from intercalation to minor groove-binding.
Publication based on the results of:
Ekaterina D. Riumina, Klink G. V., Alekseeva E. et al., PNAS, США 2026 Vol. 123 No. 35 P. 1–20
The role of escape from the cytotoxic T cell (CTL) response in SARS-CoV-2 evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the HLA class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and ...
Added: October 2, 2026
Zhukov A., Chen F., Zeng Y. et al., Nanoscale 2026 Vol. 18 No. 36 P. 19223–19253
Colloidal semiconductor nanocrystals have emerged as promising materials for next-generation light-emitting diodes (LEDs) owing to their solution processability, tunable emission wavelengths, narrow emission linewidths, and high photoluminescence quantum yields. Among them, anisotropic nanocrystals, including one-dimensional nanorods (NRs) and two-dimensional nanoplatelets (NPLs), offer additional opportunities for controlling transition dipole moment orientation and light out-coupling efficiency. These ...
Added: October 2, 2026
Мальцева В. Е., Ananyev I., Milevskii N. et al., Molecular Systems Design and Engineering 2026 Vol. 11 No. 7 P. 691–704
The use of hydrophobic deep eutectic solvents (DESs) as extractants for metal ion separation is largely due to the ease of their preparation and the possibility of modifying them depending on the composition of the metal mixture to be separated. However, the most common approach to DES modification involves the replacement of the extractant, while ...
Added: October 2, 2026
Мальцева В. Е., Ananyev I., Golubev A. V. et al., Russian Journal of Inorganic Chemistry 2026 Vol. 71 P. 724–736
Two voluminous polymer silver(I) salts of perchlorinated dodecoborate clusters, {[(Me2CO)Ag(μ-Me2CO)2Ag(Me2CO)][μ-B12Cl12]}n (1) and {[DMFAg(μ-DMF)2AgDMF][μ-B12Cl12]}n (2) were synthesized. The 35Cl nuclear quadrupole resonance (NQR) spectroscopy supplemented with the X-ray diffraction data was applied for identifying and analyzing noncovalent interactions Cl···X in these salts. Whereas in X-ray diffraction, noncovalent interactions are associated with the presence of the shortened ...
Added: October 2, 2026
Мальцева В. Е., Rozhkov A., Ananyev I. et al., Inorganic Chemistry 2026 Vol. 65 No. 22 P. 12484–12496
Despite the well-established importance of chalcogen bonding in crystal engineering and supramolecular chemistry, experimental charge density data for TeII-centered chalcogen bonds have remained entirely absent, leaving the electronic nature of these interactions uncharacterized at the level of directly measured electron density. Here, we report the first high-resolution X-ray diffraction (HRXRD) study of TeII-centered chalcogen bonds, ...
Added: October 2, 2026
Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902
Added: October 2, 2026
Ostovari Moghaddam A., Mehrabi-Kalajahi S., Solizoda I. A. et al., Metals and Materials International 2026 P. 1–9
Off-stoichiometric boron-doped chemically complex intermetallic alloys (CCIMAs) have recently emerged as a new avenue for overcoming the low temperature brittleness of ordered superlattices. However, their behavior at high temperatures remains unexplored. In this study, a novel (Ni39.6Co29.3Cr10Al15.8Ta3.3Nb2)98.5B1.5 CCIMA was prepared and its oxidation resistance over a wide temperature range (500 °C–950 °C) was studied. The ...
Added: October 1, 2026
Knyazev E., Чеботарева О. Е., М.: Издательский дом НИУ ВШЭ, 2026.
This teaching and learning guide provides a concise overview of the theoretical and practical aspects of the basic skills required to work in a biological laboratory. It also includes protocols for practical classes conducted as part of the introductory professional training placement for first-year students in the Bachelor’s programme in Cell and Molecular Biotechnology at ...
Added: September 30, 2026
Ryskina H., Knyazev E., Вопросы биологической, медицинской и фармацевтической химии 2026 Т. 29 № 9 С. 84–91
Introduction. The active integration of rapidly developing omics and computer technologies in the 21st century has led to a breakthrough in understanding the principles of the functioning of living systems. One of the dynamically developing integrative areas in biology is biological modeling. The fundamental paradigm has been the methodology that allows for the prediction of ...
Added: September 29, 2026
Kashpurovich I., Oleynichenko A., Stegailov V., Supercomputing Frontiers and Innovations 2026 Vol. 13 No. 1 P. 52–73
We report a high-performance implementation of the resolution-of-the-identity Hartree–Fock method that fully exploits the permutational symmetry of three-center electron repulsion integrals (ERI). The present implementation adopts a hybrid MPI+OpenMP parallelization strategy. Two different algorithmic approaches (with and without the pre-transformation of ERIs) are compared. A custom data layout introduced previously is employed. Designed to efficiently ...
Added: September 28, 2026
Gureev M., Advanced Science 2026 P. 1–13
Targeted protein degradation represents a promising therapeutic strategy, yet its broader application is often limited by the scarcity of usable E3 ligases. Glutathione peroxidase 4 (GPX4) is a key target for inducing ferroptosis, but achieving sustained and potent inhibition remains challenging with conventional enzymatic inhibitors. Herein, we report the first small‐molecule GPX4 degraders that incorporate ...
Added: September 26, 2026
Budkov Y., Kiselev M. G., Journal of Chemical Physics 2026 Vol. 165 No. 12 Article 124508
We develop a three-mode statistical-mechanical theory for a two-conformer
solute in a near-critical solvent. A compressible lattice model with
vacancies yields the Gaussian free-energy functional for a critical conserved
density, an orthogonal noncritical conserved mode, and the local conformer
fraction. Their couplings follow from packing and cohesive interactions,
rather than being introduced phenomenologically. Kawasaki transport of the
two conserved fields and ...
Added: September 24, 2026
Yurova P., Stenina I., Yaroslavtsev A. B., Membranes and Membrane Technologies 2026 Vol. 8 No. 1 P. 1–8
In this work, the effect of applying layers of polyethyleneimines with different molecular weights
(1300 and 25000 Da), polystyrene sulfonic acid or sodium polyacrylate on the surface of the heterogeneous
membrane MK-40 on the selectivity to singly charged ions was investigated. It is shown that the modification
leads to an increase in the selectivity coefficients P(Na+/Ca2+) and P(Li+/Mg2+), ...
Added: September 24, 2026
Корзникова Е. А., Babicheva R. I., Davletbakov A. A. et al., JOURNAL OF MATERIALS SCIENCE: MATERIALS IN ENGINEERING 2026 Vol. 21 Article 84
The influence of crack position and its size on short-range ordering (SRO) and high-temperature cyclic deformation behavior of refractory high-entropy alloy (RHEA) HfNbTiZr using bicrystal models has been investigated by combined Monte-Carlo (MC) and molecular dynamics (MD) simulations. It was revealed that the SRO process is affected not only by the crack size, namely the ...
Added: September 24, 2026
Diachkova E., Nikulin D., Кубкин Я. В. et al., American Journal of Respiratory and Critical Care Medicine 2026 Vol. 212
Accurate classification of a patient with pulmonary hypertension (PH) into one of five groups is fundamental for appropriate disease management strategies. The time from disease onset to correct diagnosis is unacceptably long in many cases. Chronic thromboembolic pulmonary hypertension (CTEPH) develops as a consequence of venous thromboemboli, resulting in a more pronounced hereditary predisposition to ...
Added: September 23, 2026
Xu Y., Ryabov F., Alexandrov I. et al., USA 2026 Vol. 6 No. 8 Article 101324
Центромеры обеспечивают расхождение хромосом, однако организацию их хроматина в пределах повторяющейся альфа-сателлитной ДНК долгое время было трудно изучать. Для решения этой задачи мы создали гаплотип-разрешённые аннотации сателлитной ДНК для полной диплоидной сборки генома человека T2T-HG002. Затем с помощью метода направленного метилирования с секвенированием длинных прочтений (DiMeLo-seq) мы картировали центромерный белок A (CENP-A), модификацию H3K9me3 и ...
Added: September 23, 2026
Hebbar P., Ryabov F., Alexandrov I. et al., Cell 2026 Vol. 189 P. 4891–4908.e12
The common marmoset is a New World monkey widely used to study primate evolution and human disease. We present a telomere-to-telomere (T2T) reference assembly for the species, plus three near-T2T haplotypes. These resolve previously inaccessible regions, including the centromeres, sex chromosomes, subterminal satellites, acrocentric chromosomes, and the major histocompatibility complex (MHC). We find marmoset centromeres ...
Added: September 23, 2026
Budkov Y., Journal of Chemical Physics 2026 Vol. 165 No. 12 Article 124105
Exact theories of electrolyte structure must satisfy the nonlocal constraints imposed by electrostatic screening, yet these constraints are most commonly formulated only for homogeneous bulk systems and at the level of two-point correlations. Here, we develop a unified field-theoretic framework that extends them to general inhomogeneous ionic fluids and nonlinear charge correlations. Using a standard ...
Added: September 22, 2026
Novikov A., Journal of Organic Chemistry 2026 Vol. 91 No. 39 P. 13108–13114
A heptafluorobutyric acid-induced cross-dehydrogenative coupling reaction of arylamines with 1,2,4-triazines has been described. This metal-free protocol enables regioselective para-C–H hetarylation of diverse arylamines including well-known fluorophore scaffolds, such as triphenylamine, carbazole, and phenothiazine, with easily accessible 1,2,4-triazines under mild conditions. This approach has potential for drug development and material design. ...
Added: September 22, 2026
Khnkoian G., Galigerov V., Grishichkin Y. et al., , in: Parallel Computational Technologies, 19th International Conference, PCT 2025, Moscow, Russia, April 8–10, 2025, Revised Selected Papers. (CCIS, volume 2891)Vol. 2891.: Springer, 2026. P. 532–545.
This work presents atomic-scale modeling of the perturbed flow of a Lennard-Jones fluid in a quasi-two-dimensional system containing one billion atoms. A statistically stationary flow regime corresponding to a Reynolds number of Re ≈ 1000 has been achieved, the flow structure has been analyzed, and the energy spectrum of velocities has been calculated. The results ...
Added: May 19, 2026
MDProcessing.jl: Julia Programming Language Application for Molecular Dynamics Trajectory Processing
Pisarev V., Panov M., , in: Supercomputing: 9th Russian Supercomputing Days, RuSCDays 2023, Moscow, Russia, September 25–26, 2023, Revised Selected Papers, Part II* 2.: Springer, 2023. P. 209–222.
Molecular simulations and molecular dynamics in particular are among the most performance-demanding computational methods. As the scale of simulations increases, the task of processing the simulation results becomes a computationally-hungry problem as well. The usual approach to build easy-to-use post-processing tools is based on providing an interface to a high-performance library called from a scripting ...
Added: November 11, 2025
Aliper E., Ryzhov I., Obukhova P. et al., Biochimica et Biophysica Acta - Biomembranes 2026 Vol. 1868 No. 1 Article 184472
Antibodies to peptide 1147 (amino acids 1147-61) of the SARS-CoV-2 protein S are highly diagnostic. Peptide 1147, although located in a region that is partly spatially hidden in the intact protein, is not subject to mutations, suggesting therapeutic potential. The aim of this study was to elucidate the architecture of this region and the way ...
Added: October 20, 2025
Volynsky P., Urban A., Pavlov K. et al., International Journal of Molecular Sciences 2025 Vol. 26 No. 2 Article 553
Alzheimer’s disease (AD) pathogenesis is correlated with the membrane content
of various lipid species, including cholesterol, whose interactions with amyloid precursor
protein (APP) have been extensively explored. Amyloid-β peptides triggering AD are
products of APP cleavage by secretases, which differ depending on the APP and secretase location
relative to ordered or disordered membrane microdomains. We used high-resolution
NMR to probe ...
Added: October 12, 2025
Махаева Г. Ф., Ковалева Н. В., Рудакова Е. В. et al., Molecules 2024 Vol. 29 No. 2 Article 321
Effective therapeutics for Alzheimer’s disease (AD) are in great demand worldwide. In our previous work, we responded to this need by synthesizing novel drug candidates consisting of 4-amino-2,3-polymethylenequinolines conjugated with butylated hydroxytoluene via fixed-length alkylimine or alkylamine linkers (spacers) and studying their bioactivities pertaining to AD treatment. Here, we report significant extensions of these studies, ...
Added: September 14, 2025