A5050974208- Computational Drug Discovery Methods
- Free Radicals and Antioxidants
- Cancer therapeutics and mechanisms
- DNA and Nucleic Acid Chemistry
- Chemical Reaction Mechanisms
- Metal complexes synthesis and properties
- Machine Learning in Materials Science
- Advanced Chemical Physics Studies
- Analytical Chemistry and Chromatography
- Phytochemicals and Antioxidant Activities
- Magnetism in coordination complexes
- Tuberculosis Research and Epidemiology
- Crystallography and molecular interactions
- Chemical Reactions and Isotopes
- Essential Oils and Antimicrobial Activity
- Advanced Chemical Sensor Technologies
- Fungal Plant Pathogen Control
- Toxic Organic Pollutants Impact
- Synthesis and biological activity
- Electrochemical Analysis and Applications
- Photochemistry and Electron Transfer Studies
- Plant biochemistry and biosynthesis
- Crystal structures of chemical compounds
- Lanthanide and Transition Metal Complexes
- X-ray Diffraction in Crystallography
Slovak University of Technology in Bratislava
2018-2024
Slovak Academy of Sciences
2024
Comenius University Bratislava
1984-1996
Flavonoids are a group of polyphenolic compounds known to possess good radical scavenging activity. It was also shown that their anti/prooxidant properties strongly structure‐dependent and can be modified by metal ion binding. The structural parameters appear key factors during DNA‐binding abilities. This work deals with spectroscopic theoretical studies two flavonoids, baicalein scutellarein, alone, in the presence redox‐active Cu(II). Cu(II) is catalytic active Fenton‐like reactions...
Abstract New type of cytotoxicity descriptors based on Cu(II) coordination ability p ‐substituted phenols and subsequent O→Cu electron density transfer is introduced. Geometries their complexes are optimized at the DFT level theory. The amount evaluated using copper charge or Laplacian Cu−O bond critical point. Cu‐phenol interaction energy a measure phenol reactivity. Statistical parameters for linear dependence published data above predictors much better than classical ones.
Herein, we present the capacity of three different molecular docking programs (AutoDock, AutoDock Vina, and PLANTS) to identify reproduce binding modes ligands in 247 covalent 169 noncovalent complex crystal structures severe acute respiratory syndrome coronavirus 2 main protease (M
Abstract The structures of camptothecin (CPT) lactone form and its complexes with Cu(II) were optimized at B3LYP/6-311G* level theory. Their electronic evaluated via QTAIM topological analysis electron density Mulliken population analysis. Stability, distribution geometrical factors the systems compared. Both CPT nitrogen atoms show lower affinity to compared oxygen ones. atom in ring one neighbouring carbonyl group highest stability Cu-CPT which indicates most probable reaction sites.
Abstract Here we present three distinct machine learning (ML) approaches (TensorFlow, XGBoost, and SchNetPack) for docking score prediction. AutoDock Vina is used to evaluate the inhibitory potential of ZINC15 in‐vivo in‐vitro‐only sets towards SARS‐CoV‐2 main protease. The set (59 884 compounds) ML training (max. 80%), validation (5%), testing (15%). (174 014 evaluation prediction capability trained models. Contributions error are analyzed with respect compounds' charge, number atoms,...
Copper(<sc>ii</sc>) complexes with flavonoids as perspective therapeutic agents DNA a target molecule.
Options to improve the extrapolation power of neural network designed using SchNetPack package with respect top docking scores prediction are presented. It is shown that hyperparameter tuning atomistic model representation (in schnetpack.representation) improves scoring compounds, which have characteristically a low incidence in randomized data sets for training machine learning models. The robustness evaluated according mean square error (MSE) and entropy average loss landscape decrease....
Abstract Geometries of camptothecin, irinotecan, SN-38, and their hypothetical Cu(II) complexes were optimized at the B3LYP/6-311G* level theory. Their electron structure, evaluated in terms Mulliken population analysis Quantum Theory Atoms-in-Molecule, was subsequently related to vitro cytotoxicity. Electron density transfer from relevant active sites Cu decreases sequence irinotecan > SN-38 camptothecin. The absolute values metal-ligand interaction energies exhibit same trend....
Abstract Structures of irinotecan (CPT-11) in neutral lactone, carboxyl, and anionic carboxylate forms singlet ground states their complexes with Cu(II) doublet are optimized using B3LYP/6-311G* treatment. Metal ion affinities (MIA), Cu charges Laplacians Cu-ligand bond critical points possible CPT active sites evaluated. The formation the ligand leads to release CO 2 that can cause a decrease concentration lactone form due equilibria between all drug. MIA values electron density transfer...
The structures of camptothecin (CPT) in neutral lactone (I), carboxyl (II) and anionic carboxylate (III) forms singlet ground states their complexes with Cu(II) doublet were optimized at B3LYP/6-311G* level theory. Metal ion affinities (MIA), Cu charges Laplacians Cu-ligand bond critical points possible CPT active sites evaluated. In most cases the electron density transfer from form III causes CO2 release thus its termination. MIA values indicate that this exhibits significantly higher...
The geometries of camptothecin, irinotecan, SN-38, and their hypothetical Cu(II) complexes are optimized at the B3LYP/6-311G* level theory. Their electron structure, evaluated in terms Mulliken population analysis Quantum Theory Atoms-in-Molecule, is subsequently related to vitro cytotoxicity. density transfer from relevant active sites Cu decreases sequence irinotecan > SN-38 camptothecin. absolute values metal-ligand interaction energies exhibit same trend. discrepancy with least relative...
Cytotoxicity of camptothecin (CPT) in neutral lactone form (I) and its most stable forms protonated at pyridine nitrogen (II) pyridone oxygen (III), which is much less stable, investigated the B3LYP/6-311G* level theory. The structures their hypothetical Cu(II) complexes were optimized. reduced experimental cytotoxicity CPT salts rationalized terms metal-ion affinities, Cu charges, electron-density Laplacians Cu-ligand bond critical points. Electron density transfer to occurs predominantly...
The geometries of camptothecin, irinotecan, SN-38, and their hypothetical Cu(II) complexes are optimized at the B3LYP/6-311G* level theory. Their electron structure, evaluated in terms Mulliken population analysis Quantum Theory Atoms-in-Molecule, is subsequently related to vitro cytotoxicity. density transfer from relevant active sites Cu decreases sequence irinotecan > SN-38 camptothecin. absolute values metal-ligand interaction energies exhibit same trend. discrepancy with least relative...