Docking and Molecular Dynamics Studies on DNA-Heterocyclic Enediynes Interaction to Identify the Preferred Binding Mode

M. A. Gureev; Danilkina N. A.; Khlebnikov A. F.; Balova I. A.

doi:10.1134/S1070363224140111

Publications

?

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.

M. A. Gureev, Danilkina N. A., Khlebnikov A. F., Balova I. A.

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.

Research target: Chemistry Biology

Keywords: Molecular Docking molecular dynamics enediyne antibiotics

Publication based on the results of:

Molecular evolution, protein motions and computational molecular modeling (2024)

Surface-sulfonated Al₂O₃, CeO₂, and TiO₂ as functional fillers for Nafion-type gel polymer electrolytes for lithium metal batteries

Voropaeva D., S. Novikova, I. Stenina et al., Solid State Ionics 2026 Vol. 445 Article 117288

Composite gel polymer electrolytes based on a perfluorinated sulfonic acid cation-exchange MF-4SC membrane containing surface-sulfonated nanoparticles of aluminum oxide, cerium (IV) oxide, and titanium oxide (sAl2O3, sCeO2, and sTiO2, respectively) were prepared by casting from a dispersion in N,N-dimethylformamide and plasticized with a 1,3-dioxolane/1,2-dimethoxyethane mixture. The influence of the filler nature on ionic conductivity, solvent uptake, activation energy, lithium ...

Added: July 30, 2026

EEG evidence for reproducible neural states during Buddhist Highest Yoga Tantra meditation

Mikhaylets E. V., Razorenova A. М., Chernyshev V. L. et al., Scientific Reports 2026 Vol. 16 Article 23560

Meditation offers a naturalistic paradigm for studying introspection, yet the neural dynamics of advanced tantric practices remain largely unexplored. Buddhist Highest Yoga Tantra (BHYT) comprises a sequence of eight dissolution stages culminating in the “clear light” state. We recorded EEG during eyes-closed BHYT meditation performed in monasteries and hermitages (51 sessions from 36 male practitioners; ...

Added: July 29, 2026

Long-range machine-learning potentials with environment-dependent charges enable predicting LO-TO splitting and dielectric constants

Korogod D., Shapeev A., Ivan S. Novikov, Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 114 No. 2 Article 024104

We present two models with explicit long-range electrostatics in the form of Coulomb interactions. Both models include point charges depending on their local atomic environments, and the second model also conserves a total charge of an atomic system. We combine the proposed long-range models with the local moment tensor potential (MTP) and demonstrate that they ...

Added: July 22, 2026

Особенности потенциала, следующего за частотой, зарегистрированного в ответ на изменения в параметрах звучания речевого сигнала (изолированного слога)

Окнина Л. Б., Подлепич В. В., Sieber I. et al., Физиология человека 2026 Т. 52 № 3 С. 5–15

The aim of this study was to evaluate the frequency following response (FFR) for the analysis of the intact perception of syllables in humans. For this purpose, event-related potentials (ERPs) in response to isolated Russian syllables were recorded and analyzed in 29 healthy persons in two frequency ranges, standard (1-40 Hz) and high frequency (70-150 ...

Added: June 30, 2026

A Way to Create Mn-Containing GdFe3(BO3)4 and the Dopant Effect on Its Magnetic Properties

Moshkina E., Molokeev M., Zolotov A. et al., Journal of Alloys and Compounds 2026 Vol. 1077 Article 189412

A wide series of substitutions in a subsystem of small radii cations M = Al, Cr, Fe, Ga, Sc is possible in rare-earth borates ReM3(BO3)4 with the huntite structure. However, the existence of these compounds where M = Mn still raises doubts. The study presents a synthetic approach developed in the framework of the flux method allowing for the required ...

Added: June 29, 2026

Incorporating Scientific Knowledge into Neural Network Density Functionals

Schneider M., Zaripov D., Dokin R. et al., Journal of Chemical Theory and Computation 2026 Vol. 22 No. 9 P. 4405–4414

Density functional theory (DFT) is the workhorse of modern reactions and materials modeling. While the exact functional remains unknown, many approximations to it have been constructed either by hand-crafting functional forms to satisfy exact constraints or by machine learning. In this work, we show how both of these approaches can be fused to build both ...

Added: June 26, 2026

Electrodeposition and electrochromic properties of hydrated mixed oxides MoxW1-xO3·2H2O films

Laurinavichyute V., Levin E. E., Mironkova A. A. et al., Surfaces and Interfaces 2026 Vol. 81 Article 108389

In this work we characterize mixed Mo-W acidic deposition solutions with Mo content ranging from 0 to 100 mol.% by Raman and UV–Vis spectroscopy. The obtained distribution diagram of mixed isopolyanions allows one to explain the observed change in film deposition rate with increase in Mo content. It was found that the initial decrease in ...

Added: June 24, 2026

Эволюция, экология, генетика человека, медицинская паразитология. Практикум.

Ryskina H., Лобаева Т. А., Ануркина А. И., Ваш формат, 2025.

Я Эволюция, экология, генетика человека, медицинская паразитология. Практикум. Аннотация Аннотация к практикуму «Эволюция, экология, генетика человека, медицинская паразитология» Учебное пособие «Эволюция, экология, генетика человека, медицинская паразитология. Практикум» (авторы: Лобаева Т. А., Рыскина Е. А., Ануркина А. И.; издательство «Ваш формат», 2025 год, 194 страницы) предназначено для студентов высших учебных заведений. Цель практикума — обеспечить комплексное освоение ключевых разделов биологии с акцентом на их прикладное значение в медицине. ...

Added: June 23, 2026

Zα and Zβ Localize ADAR1 to Flipons That Modulate Innate Immunity, Alternative Splicing, and Nonsynonymous RNA Editing

Herbert A., Cherednichenko O., Lybrand T. et al., International Journal of Molecular Sciences 2025 Vol. 26 No. 6 Article 2422

The double-stranded RNA editing enzyme ADAR1 connects two forms of genetic programming, one based on codons and the other on flipons. ADAR1 recodes codons in pre-mRNA by deaminating adenosine to form inosine, which is translated as guanosine. ADAR1 also plays essential roles in the immune defense against viruses and cancers by recognizing left-handed Z-DNA and ...

Added: June 22, 2026

Embryonic enhancers help transmit positional information to the initiator cores that control Drosophila Abd-B regulatory domains

Kyrchanova O., Kudryashova K., Ibragimov A. et al., Development 2025 Vol. 152 No. 19 P. 1–12

Drosophila homeotic gene Abdominal-B (Abd-B) is controlled throughout development by four infraabdominal (iab) regulatory domains, the active or repressed state of which is determined by initiators that have parasegment-specific enhancer activity at an early stage of embryonic development. For this reason, it has long been assumed that the enhancer activity and initiation function of these elements are synonymous. ...

Added: June 20, 2026

Initiators counteract Polycomb repression and stimulate long-range contacts between enhancers and the Abdominal-B promoter in Drosophila

Kyrchanova O., Ksenia Kudryashova, Dubrovskaya V. et al., Open Biology 2025 Vol. 15 No. 11 Article 250192

The specification of abdominal segments A5 to A9 depends on the expression of Abdominal-B (Abd-B), which is regulated by four infraabdominal domains: iab-5 through iab-8,9. Each iab domain contains an initiation element that determines its active state, along with enhancers responsible for tissue-specific activation of Abd-B. These iab domains function autonomously due to their flanking boundaries, Fab-6, Fab-7 and Fab-8, which both block crosstalk between adjacent iab domains (insulator function) and facilitate long-range ...

Added: June 20, 2026

Construction of Promoter Elements for Strong, Moderate, and Weak Gene Expression in Drosophila melanogaster

Kudryashova K.S., Deriglazova I. O., Osadchiy I. S. et al., Genes 2025 Vol. 16 No. 1 Article 3

Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, ...

Added: June 20, 2026

Diverse β-bungarotoxin isoforms manifest different affinities to voltage-gated potassium channels of Kv1.x subfamily

Ksenia Kudryashova, Filippova E., Kryukova E. et al., Archives of Biochemistry and Biophysics 2025 Vol. 769 Article 110437

β-Bungarotoxins (β-BuTx), consisting of covalently bound phospholipase A2 subunit (A-chain), a member of group Ia of secretory phospholipases A2, and non-enzymatic subunit (B-chain) structurally related to Kunitz-type protease inhibitors, block presynaptic neuromuscular transmission via a not completely defined mechanism of action. In vivo physiological studies revealed that the B-chain is targeting voltage-gated potassium channels of not identified subtypes. In our work, six β-BuTx isoforms were ...

Added: June 20, 2026

Benchmarking DNA large language models on quadruplexes

Cherednichenko O., Herbert A., Poptsova M., Computational and Structural Biotechnology Journal 2025 Vol. 27 P. 992–1000

Large language models (LLMs) in genomics have successfully predicted various functional genomic elements. While their performance is typically evaluated using genomic benchmark datasets, it remains unclear which LLM is best suited for specific downstream tasks, particularly for generating whole-genome annotations. Current LLMs in genomics fall into three main categories: transformer-based models, long convolution-based models, and state-space models ...

Added: June 19, 2026

Kolmogorov–Arnold networks for genomic tasks

Cherednichenko O., Poptsova M., Briefings in Bioinformatics 2025 Vol. 26 No. 2 Article bbaf129

Kolmogorov–Arnold networks (KANs) emerged as a promising alternative for multilayer perceptrons (MLPs) in dense fully connected networks. Multiple attempts have been made to integrate KANs into various deep learning architectures in the domains of computer vision and natural language processing. Integrating KANs into deep learning models for genomic tasks has not been explored. Here, we ...

Added: June 19, 2026

Molecular biology of the deadliest cancer – glioblastoma: what do we know?

Aly Ismailov, Spallone A., Belogurov A. et al., Frontiers in Immunology 2025 Vol. 16 Article 1530305

Glioblastomas are the most prevalent primary brain tumors and are associated with a dramatically poor prognosis. Despite an intensive treatment approach, including maximal surgical tumor removal followed by radio- and chemotherapy, the median survival for glioblastoma patients has remained around 18 months for decades. Glioblastoma is distinguished by its highly complex mechanisms of immune evasion ...

Added: June 17, 2026

Unique morphology and ecology lifestyle of a new craniiform brachiopod from the Upper Ordovician of Estonia (Baltica)

Madison A., Plandin F., Kuzmina T. et al., Palaeogeography, Palaeoclimatology, Palaeoecology 2026 Vol. 697 Article 113864

Unlike most other brachiopods, craniiforms lack a prominent pedicle, cement to a hard substrate by their ventral valve, and thereby can be easily distinguished in paleontological materials. In this study, we describe a new genus and species from the Porkuni Regional Stage of Northeastern Estonia (Baltica), corresponding to the lower part of the Hirnantian Stage ...

Added: June 15, 2026

Does the pedicle exist in craniiform brachiopods?

Plandin F., Temereva E., Zoological Journal of the Linnean Society 2025 Vol. 205 No. 2 Article zlaf139

Although Brachiopoda represent a relatively small phylum, they exhibit significant morphological diversity. One of the central issues in understanding the evolution of the ancestral brachiopod body plan pertains to the homologies among body compartments across the different brachiopod subphyla: Craniiformea, Linguliformea, and Rhynchonelliformea. In this context, the pedicle stands out as one of the most ...

Added: June 15, 2026

Impact of heat treatment on microstructure and mechanical properties of additively manufactured aluminum bronze

Filippova A. V., Yurchenko N. Y., Smirnov S. A. et al., Journal of Alloys and Compounds 2026 No. 1074 Article 189162

This study investigates the effects of post-processing heat treatment at 300–500 °C on the microstructure, hardness, and tensile properties of laser powder bed fusion (PBF-LB) processed Al-bronze processed with energy densities (ED) in the range of 125–938 J/mm3. In the as-printed state, sharp needle-like α + β′ laths form at lower ED whereas with increasing ED, the β′ ...

Added: June 12, 2026

Microbial diversity and production of milk spirit using traditional Buryat fermentation and distillation technologies

Namsaraev Z., Nanzatov B., Kozlova A. et al., Scientific Reports 2026 Vol. 16 No. 1 Article 17769

Distilled fermented milk beverages are rare in food technology, despite the global prevalence of plant-based spirits. Currently, the production of distilled strong alcoholic beverages from fermented milk using traditional technologies is known only among Mongolic-speaking peoples and their Siberian neighbors. This study provides the first interdisciplinary analysis of darasun, a traditional Buryat spirit made from fermented ...

Added: June 10, 2026

Scaling Up Molecular Hydrodynamics of Non-Laminar Flows with GPU-Aware MPI

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

Immune Antibodies Recognizing the Stem Region of SARS-CoV-2 Spike Protein: Molecular Modelling and In Vitro Study of Synthetic Peptides Presentation to the Antibodies

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

Diverse Interactions of Sterols with Amyloid Precursor Protein Transmembrane Domain Can Shift Distribution Between Alternative Amyloid-β Production Cascades in Manner Dependent on Local Lipid Environment

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