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Cobra cardiotoxins: membrane interactions and pharmacological potential
Current Medicinal Chemistry. 2013. Vol. 21. No. 3. P. 270–287.
Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, СTs) from cobra venom. They are fully b-structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to lipid bilayer was shown to depend on amino acid sequence in the tips of the three loops. In the present review, CT-membrane interactions are analyzed through the prism of data on binding of the toxins to phospholipid liposomes and detergent micelles, as well as their structural and computational studies in membrane mimicking environments. We assess different hydrophobicity scales to compare membrane partitioning of various CTs and their membrane effects. A comparison of hydrophobic/hydrophilic properties of CTs and linear polycationic peptides provides a key to their biological activity and reveal rationality for design of new membrane-interacting compounds. Finally, since the viewpoint of the data obtained on model lipid membranes, cytotoxic activity of CTs against cancer cells is discussed.
Shabanov N., Kuricheva O., Kurbatova J. et al., / Series Working Papers SSRN "Department of Economics Ca’ Foscari University of Venice". 2026.
The carbon balance of an ecosystem is the difference between Gross Primary Productivity (GPP) and Ecosystem Respiration (Reco) as expressed by Net Ecosystem Exchange (NEE). While remote sensing retrievals of GPP have reached maturity, Reco estimation remains underexplored and ultimately cast bias on NEE. Here we present an end-to-end multi-scale analysis of the mechanism of ...
Added: August 21, 2026
Ponomarenko A., / Series Computer Science "arxiv.org". 2025.
This paper addresses the challenge of merging hierarchical navigable small world (HNSW) graphs, a critical operation for distributed systems, incremental indexing, and database compaction. We propose three algorithms for this task: Naive Graph Merge (NGM), Intra Graph Traversal Merge (IGTM), and Cross Graph Traversal Merge (CGTM). These algorithms differ in their approach to vertex selection ...
Added: July 30, 2026
Piontkovski D., / Series arXiv "math". 2026.
A noncommutative projective variety is defined, following Artin and Zhang, by a graded coherent algebra 𝐴. The category of coherent sheaves is then the quotient qgr(𝐴) of the category of finitely presented graded modules by the subcategory of torsion modules. We consider the categorical and polynomial entropies of the Serre twist, that is, of the ...
Added: June 23, 2026
Piontkovski D., / Series arXiv "math". 2025.
If a symmetric multilinear algebra is weakly nil, then it is Engel. This result may be regarded as an infinite-dimensional analogue of the well-known Jacobian theorem, which states that if a polynomial mapping has a polynomial inverse, then its Jacobian matrix is invertible. This refines a theorem of Gerstenhaber and partially answers a question posed ...
Added: June 23, 2026
Vanhaelen Q., Lin Y., Zhavoronkov A., ACS Medicinal Chemistry Letters 2020 Vol. 11 No. 8 P. 1496–1505
Generative adversarial networks (GANs), first published in 2014, are among the most important concepts in modern artificial intelligence (AI). Bridging deep learning and game theory, GANs are used to generate or “imagine” new objects with desired properties. Since 2016, multiple GANs with reinforcement learning (RL) have been successfully applied in pharmacology for de novo molecular design. Those ...
Added: June 1, 2026
Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.
A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.
Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...
Added: April 20, 2026
Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...
Added: April 2, 2026
Sorokin K., Beketov M., Онучин А. et al., / arxiv.org. Серия cs.SI "Social and Information Networks ". 2025.
Community detection in complex networks is a fundamental problem, open to new approaches in various scientific settings. We introduce a novel community detection method, based on Ricci flow on graphs. Our technique iteratively updates edge weights (their metric lengths) according to their (combinatorial) Foster version of Ricci curvature computed from effective resistance distance between the ...
Added: January 15, 2026
Petrovanov I., Sergeev A., / Series Computer Science "arxiv.org". 2025. No. 2512.18332.
Transport coding reduces message delay in packet-switched networks by introducing controlled redundancy at the transport layer: original packets are encoded into coded packets, and the message is reconstructed after the first successful deliveries, effectively shifting latency from the maximum packet delay to the -th order statistic. We present a concise, reproducible discrete-event implementation of transport coding in OMNeT++, including ...
Added: December 24, 2025
Hessian-based lightweight neural network for brain vessel segmentation on a minimal training dataset
Меньшиков И. А., Бернадотт А. К., Elvimov N. S., / Series arXie "Statistical mechanics". 2025.
Accurate segmentation of blood vessels in brain magnetic resonance angiography (MRA) is essential for successful surgical procedures, such as aneurysm repair or bypass surgery. Currently, annotation is primarily performed through manual segmentation or classical methods, such as the Frangi filter, which often lack sufficient accuracy. Neural networks have emerged as powerful tools for medical image ...
Added: December 1, 2025
Aliper E. T., Efremov R., Biochimica et Biophysica Acta - Biomembranes 2025 Vol. 1867 No. 8 Article 184445
The coronavirus spike protein, the key entity effectuating membrane fusion, cannot exist without membraneactive
fragments. In addition to fusion peptides, among such domains are HR1 and HR2. Crucial to the spike’s
refolding and membrane fusion, they are believed to both interact with each other and bind to the membranes
that are merged. To elucidate HR2’s precise role in ...
Added: October 12, 2025
Konshina A., Bocharov E., Konovalova E. et al., International Journal of Molecular Sciences (Швейцария) 2024 Vol. 25 No. 21 Article 11370
Non-immunoglobulin-based scaffold proteins (SPs) represent one of the key therapeutic
target-specific and high-affinity binders in modern medicine. Among their cellular targets are signaling
receptors, in particular, receptor tyrosine kinases, whose dysfunction leads to the development
of cancer and other serious diseases. Successful applications of SPs have been reported for
HER receptor type 2 (HER2), a member of the human ...
Added: December 9, 2024
Svitanko I. V., Novikov F. N., Medvedev M. G., , in: XXII Mendeleev Congress on General and Applied Chemistry, October 7-12, 2024, Federal Territory “Sirius”, Russia. Book of abstracts in 7 volumesVol. 5.: “Admiral Print” LLC, 2024.
ADD-ONS TO MOLECULAR MODELING METHODS: IMPROVEMENT IN ACTIVITY PREDICTION ...
Added: October 14, 2024
Aliper E., Roman G. Efremov, International Journal of Molecular Sciences 2023 Vol. 24 No. 22 Article 16421
Membrane-spanning portions of proteins’ polypeptide chains are commonly known as
their transmembrane domains (TMDs). The structural organisation and dynamic behaviour of TMDs
from proteins of various families, be that receptors, ion channels, enzymes etc., have been under
scrutiny on the part of the scientific community for the last few decades. The reason for such attention
is that, apart from ...
Added: September 15, 2024
Fedulova A., Armeev G., Romanova T. et al., Wiley Interdisciplinary Reviews: Computational Molecular Science 2024 Vol. 14 No. 4 Article e1728
Understanding the function of eukaryotic genomes, including the human genome, is undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of eukaryotic genome organization is nucleosomes—elementary building blocks of chromatin about 10 nm in size that wrap DNA around an octamer of histone proteins. Nucleosomes are integral players in all genomic processes, ...
Added: August 29, 2024
I. V. Svitanko, Pivina T. S., Russian Chemical Bulletin 2024 Vol. 73 No. 5 P. 1093–1108
The review gives a retrospective of methods for molecular modeling of the structures, mechanisms of chemical reactions, and properties of organic compounds. The development and advancement of the ideology of preliminary modeling of the structures and formation mechanisms of reaction products in the planning of any synthesis is a relevant task in this fi eld of science. Some ...
Added: June 21, 2024
Krasavin M., Peshkov A., Lukin A. et al., International Journal of Molecular Sciences 2022 Vol. 23 No. 19 Article 11579
Starting from a screening hit, a set of analogs was synthesized based on a 4-(2-aminoethyl)piperidine core not associated previously with trace amine-associated receptor 1 (TAAR1) modulation in the literature. Several structure–activity relationship generalizations have been drawn from the observed data, some of which were corroborated by molecular modeling against the crystal structure of TAAR1. The ...
Added: February 8, 2024
Yarovaya O., Filimonov A., Baev D. et al., Viruses 2024 Vol. 16 No. 2 Article 215
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (−)-usnic acid and studied their ability to inhibit the main ...
Added: January 31, 2024
Rusina P., Gandalipov E., Abdyusheva Y. et al., Cancers 2023 Vol. 15 No. 15 Article 3766
General toxicity for the organism is a major drawback of anticancer drugs. Development of new generation chemotherapeutics requires the knowledge about macromolecules critical for tumor cell viability. Among these species (called therapeutic targets), the protein kinases are the established enzymes. However, the parts of protein kinases that are supposed to be targeted by drugs can ...
Added: November 1, 2023
Nikita A. Kosarim, Armeev G., Alexey K. Shaytan et al., Supercomputing Frontiers and Innovations 2022 Vol. 9 No. 2 P. 56–67
The nucleosome is the basic unit of eukaryotic DNA compaction. It consists of about 147 base pairs wrapped around an octamer of histone proteins. Nucleosomal dynamics provides the availability of packaged DNA for various factors that carry out the vital processes associated with chromatin. It is not completely known how the structure and dynamics of ...
Added: September 4, 2023
Glushak A., Smirnov G., Applied Clay Science 2023 Vol. 243 Article 107072
Friedel’s salt, also known as Cl-Hydrocalumite, (Ca2[Al(OH)6]⋅ Cl⋅2H2O), is one of the calcium aluminates phases (AFm phases). It can accommodate radioactive chlorine isotopes, serving as a potential material in radioactive waste applications. Earlier X-Ray diffraction and nuclear magnetic resonance (NMR) experiments demonstrated the existence of the first-order phase transition between 303 K and 313 K. The ...
Added: July 31, 2023
van Tilborg D., Grisoni F., Journal of Chemical Information and Modeling 2022 Vol. 62 No. 23 P. 5938–5951
Machine learning has become a crucial tool in drug discovery and chemistry at large, e.g., to predict molecular properties, such as bioactivity, with high accuracy. However, activity cliffs─pairs of molecules that are highly similar in their structure but exhibit large differences in potency─have received limited attention for their effect on model performance. Not only are these ...
Added: December 22, 2022