A5069998562- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- Advanced Chemical Sensor Technologies
- Protein Structure and Dynamics
- Isotope Analysis in Ecology
- Phase Equilibria and Thermodynamics
- Chemical Thermodynamics and Molecular Structure
- Protein Degradation and Inhibitors
- Bioinformatics and Genomic Networks
- Click Chemistry and Applications
- Machine Learning in Materials Science
- Advanced Battery Materials and Technologies
- Molecular spectroscopy and chirality
- Quality and Safety in Healthcare
- Design Education and Practice
- Free Radicals and Antioxidants
- Metal complexes synthesis and properties
- Thermodynamic properties of mixtures
- Histone Deacetylase Inhibitors Research
- Chronic Lymphocytic Leukemia Research
- Ubiquitin and proteasome pathways
- Cholinesterase and Neurodegenerative Diseases
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Synthesis and biological activity
Institute of Molecular and Translational Medicine
2019-2024
Palacký University Olomouc
2019-2024
Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
2023-2024
Czech Academy of Sciences
2023-2024
Université de Strasbourg
2017-2019
National Academy of Sciences of Ukraine
2015-2017
Physical-Chemical Institute O. Bogatsky
2015-2016
Structural alerts are widely accepted in chemical toxicology and regulatory decision support as a simple transparent means to flag potential hazards or group compounds into categories for read-across. However, there has been growing concern that disproportionally too many chemicals toxic, which questions their reliability toxicity markers. Conversely, the rigorously developed properly validated statistical QSAR models can accurately reliably predict of chemical; however, use hampered by lack...
Pharmacophore models are widely used for the identification of promising primary hits in compound large libraries. Recent studies have demonstrated that pharmacophores retrieved from protein-ligand molecular dynamic trajectories outperform a single crystal complex structure. However, number can be enormous, thus, making it computationally inefficient to use all them virtual screening. In this study, we proposed selection distinct representative by removal with identical three-dimensional...
Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines needed extract relevant information from raw spectral and convert it into a more comprehensible format. Based on the sample type and/or goal of study, variety platforms can be used for such analysis. MZmine is open-source software processing generated by different platforms: liquid chromatography–MS (LC–MS), gas (GC–MS),...
Causal inference methods are helpful with finding possible biological mechanisms of nanoparticles' toxicity.
Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines needed extract relevant information from raw spectral and convert it into a more comprehensible format. Based on the sample type and/or goal of study, variety platforms can be used for such analysis. MZmine is open-source software processing generated by different platforms: liquid chromatography–MS (LC–MS), gas (GC–MS),...
Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein-ligand complexes. Due to its versatility speed, GROMACS stands out commonly utilized software platform executing molecular simulations. However, effective utilization requires substantial expertise in configuring, executing, interpreting trajectories. Existing automation tools are constrained their capability conduct large sets compounds with minimal user intervention,...
Estradiol dimers (EDs) possess significant anticancer activity by targeting tubulin dynamics. In this study, we synthesised 12 EDs variants via copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, focusing on structural modifications within the aromatic bridge connecting two estradiol moieties. vitro testing of these revealed a marked improvement in selectivity towards cancerous cells, particularly for ED1–8. The most active compounds, ED3 (IC50 = 0.38 μM CCRF-CEM) and ED5 0.71...
Abstract Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein–ligand complexes. Due to its versatility speed, GROMACS stands out commonly utilized software platform executing molecular simulations. However, effective utilization requires substantial expertise in configuring, executing, interpreting trajectories. Existing automation tools are constrained their capability conduct large sets compounds with minimal user...
Microtubule dynamic is exceptionally sensitive to modulation by small-molecule ligands. Our previous work presented the preparation of microtubule-targeting estradiol dimer (ED) with anticancer activity. In present study, we explore effect selected linkers on biological activity dimer. The were designed as five-atom chains carbon, nitrogen or oxygen in their centre. addition, central was modified a benzyl group hydroxy methoxy substituents and one derivative possessed an extended linker...
Abstract Rational approach towards the QSAR/QSPR modeling requires descriptors to be computationally efficient, yet physically and chemically meaningful. On basis of existing simplex representation molecular structure (SiRMS) novel ‘quasi‐mixture’ were developed in order accomplish goal characterization molecules on 2D level (i.e. without explicit generation 3D exhaustive conformational search) with account for potential intermolecular interactions. The critical properties organic compounds...
We report the building, validation and release of QSPR (Quantitative Structure Property Relationship) models aiming to guide design new solvents for next generation Li-ion batteries. The dataset compiled from literature included oxidation potentials (Eox ), specific ionic conductivities (κ), melting points (Tm ) boiling (Tb 103 electrolytes. Each resulting consensus assembled 9-19 individual Support Vector Machine built on different sets ISIDA fragment descriptors.(1) They were implemented...
Abstract In this article we consider the application of Transductive Ridge Regression (TRR) approach to structure‐activity modeling. An original procedure TRR parameters optimization is suggested. Calculations performed on 3 different datasets involving two types descriptors demonstrated that outperforms its non‐transductive analogue (Ridge Regression) in more than 90 % cases. The most significant transductive effect was observed for small datasets. This suggests transduction may be...
Abstract In this article we developed a system of the predictive models for second virial coefficients pure compounds. Second coefficient is property derived from equation state, and particular interest as it describes pair intermolecular interactions. The two‐layer QSPR were developed, which exploited well‐known physical equations allowed us to include information into traditional methodology. This shows some new perspectives work with temperature‐dependent properties. It was shown that 2D...
The second virial cross-coefficient is an important characteristic of the pair intermolecular interactions that describes solely heterogeneous interactions. In current study, authors made first attempt to develop rigorous QSPR models for analysis and prediction cross-coefficient. Novel descriptors describe were implemented. Statistical characteristics obtained showed high performance. Prediction errors are comparable data. Theoretically predicted values may be used derive PVT-properties...
Abstract We investigated the development and anticancer efficacy of novel estradiol dimers (ED), targeting dynamics microtubules—an essential factor in effective cancer therapy. Employing copper-catalyzed azide-alkyne cycloaddition (CuAAC), two distinct series ED variants were synthesized. The initial included thirteen dimers, derived from 17α-ethinyl estradiol, incorporating varied five-atom linkers with central carbon, nitrogen, or oxygen atoms, and, some instances, modified benzyl groups...