BACKGROUND: Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited. RESULTS: We have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set ([Formula: see text]) and also on a test set ([Formula: see text]). They are applicable for at least 95 % of molecules in key drug databases (DrugBank, ChEMBL, Pubchem and ZINC) compared to less than 60 % of the molecules from these databases for which currently used EEM parameters are applicable. CONCLUSIONS: We developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation (http://ncbr.muni.cz/eem_parameters). It enables the direct application of EEM in chemoinformatics.

• Klíčová slova
• Drug-like molecules, EEM, Electronegativity Equalization Method, Partial atomic charges, QM, Quantum mechanics,
• Publikační typ
• časopisecké články MeSH

• Publikační typ
• časopisecké články MeSH

Ferroptosis is a regular cell death pathway that has been proposed as a suitable therapeutic target in cancer and neurodegenerative diseases. Since its definition in 2012, a few hundred ferroptosis modulators have been reported. Based on a literature search, we collected a set of diverse ferroptosis modulators and analyzed them in terms of their structural features and physicochemical and drug-likeness properties. Ferroptosis modulators are mostly natural products or semisynthetic derivatives. In this review, we focused on the abundant subgroup of polyphenolic modulators, primarily phenylpropanoids. Many natural polyphenolic antioxidants have antiferroptotic activities acting through at least one of the following effects: ROS scavenging and/or iron chelation activities, increased GPX4 and NRF2 expression, and LOX inhibition. Some polyphenols are described as ferroptosis inducers acting through the generation of ROS, intracellular accumulation of iron (II), or the inhibition of GPX4. However, some molecules have a dual mode of action depending on the cell type (cancer versus neural cells) and the (micro)environment. The latter enables their successful use (e.g., apigenin, resveratrol, curcumin, and EGCG) in rationally designed, multifunctional nanoparticles that selectively target cancer cells through ferroptosis induction.

• Klíčová slova
• cancer, drug-likeness, ferroptosis, inducers, inhibitors, neurodegenerative, polyphenol,
• MeSH
• antioxidancia farmakologie   MeSH
• biologické přípravky * farmakologie   MeSH
• buněčná smrt MeSH
• cheminformatika MeSH
• ferroptóza * MeSH
• lidé MeSH
• nádory * MeSH
• reaktivní formy kyslíku metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• antioxidancia MeSH
• biologické přípravky * MeSH
• reaktivní formy kyslíku MeSH

Metformin, the first drug chosen to be tested in a clinical trial aimed to target the biology of aging per se, has been clinically exploited for decades in the absence of a complete understanding of its therapeutic targets or chemical determinants. We here outline a systematic chemoinformatics approach to computationally predict biomolecular targets of metformin. Using several structure- and ligand-based software tools and reference databases containing 1,300,000 chemical compounds and more than 9,000 binding sites protein cavities, we identified 41 putative metformin targets including several epigenetic modifiers such as the member of the H3K27me3-specific demethylase subfamily, KDM6A/UTX. AlphaScreen and AlphaLISA assays confirmed the ability of metformin to inhibit the demethylation activity of purified KDM6A/UTX enzyme. Structural studies revealed that metformin might occupy the same set of residues involved in H3K27me3 binding and demethylation within the catalytic pocket of KDM6A/UTX. Millimolar metformin augmented global levels of H3K27me3 in cultured cells, including reversion of global loss of H3K27me3 occurring in premature aging syndromes, irrespective of mitochondrial complex I or AMPK. Pharmacological doses of metformin in drinking water or intraperitoneal injection significantly elevated the global levels of H3K27me3 in the hepatic tissue of low-density lipoprotein receptor-deficient mice and in the tumor tissues of highly aggressive breast cancer xenograft-bearing mice. Moreover, nondiabetic breast cancer patients receiving oral metformin in addition to standard therapy presented an elevated level of circulating H3K27me3. Our biocomputational approach coupled to experimental validation reveals that metformin might directly regulate the biological machinery of aging by targeting core chromatin modifiers of the epigenome.

• Klíčová slova
• aging, cancer, chemoinformatics, computational screening, metformin,
• MeSH
• biokatalýza MeSH
• experimentální nádory farmakoterapie   metabolismus   MeSH
• histondemethylasy antagonisté a inhibitory   metabolismus   MeSH
• inhibitory enzymů chemie   farmakologie   MeSH
• jaderné proteiny antagonisté a inhibitory   metabolismus   MeSH
• lidé MeSH
• ligandy MeSH
• metformin chemie   farmakologie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• myši knockoutované MeSH
• myši MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• histondemethylasy MeSH
• inhibitory enzymů MeSH
• jaderné proteiny MeSH
• KDM6A protein, human MeSH Prohlížeč
• ligandy MeSH
• metformin MeSH
• Utx protein, mouse MeSH Prohlížeč

Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, current molecular design capabilities that inform medicinal chemistry decisions on peptide programs are limited. More specifically, there are unmet needs for structure-activity relationship (SAR) analysis and visualization of linear, cyclic, and cross-linked peptides containing non-natural motifs, which are widely used in drug discovery. To bridge this gap, we developed PepSeA (Peptide Sequence Alignment and Visualization), an open-source, freely available package of sequence-based tools (https://github.com/Merck/PepSeA). PepSeA enables multiple sequence alignment of non-natural amino acids and enhanced visualization with the hierarchical editing language for macromolecules (HELM). Via stepwise SAR analysis of a ChEMBL peptide data set, we demonstrate the utility of PepSeA to accelerate decision making in lead optimization campaigns in pharmaceutical setting. PepSeA represents an initial attempt to expand cheminformatics capabilities for therapeutic peptides and to enable rapid and more efficient design-make-test cycles.

• MeSH
• cheminformatika MeSH
• peptidy * chemie   MeSH
• proteiny * MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• peptidy * MeSH
• proteiny * MeSH

• Klíčová slova
• chemoinformatics, computational chemistry, computational methods in medicinal chemistry, computer-aided-drug design, drug discovery, molecular modeling, web-servers,
• Publikační typ
• úvodníky MeSH

Use of 'green biomass' of the grapevine is gradually extending into the food industry. The aim of our study was to demonstrate the potential of metabolomic fingerprinting for characterization of grapevine leaves and canes. Our method comprises successive aqueous-methanolic extractions, followed by U-HPLC-HRMS/MS. For data processing, PCA and (O)PLS-DA methods were utilized, and mathematical models were validated. We showed that from all factors investigated, harvesting season explained most of the variability between samples, followed by locality combined with farming system. The identified statistically significant metabolites for harvesting season models mostly represented the groups of fatty acids, fatty phenols, (lyso)phospholipids, flavonoids and organic acids. For models of localities with different farming systems, majority of identified metabolites significant for organic farming belonged to groups of fatty acids and their derivatives, terpenoids, sterols, and fat soluble vitamins, whereas for conventional farming, the only identified significant metabolites were the pesticide residues.

• Klíčová slova
• Authenticity, Canes, Grapevine, Leaves, Metabolomics, Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry, Vitis vinifera,
• MeSH
• analýza potravin metody   statistika a číselné údaje   MeSH
• biomasa MeSH
• biozemědělství MeSH
• cheminformatika metody   MeSH
• fenoly analýza   metabolismus   MeSH
• flavonoidy analýza   metabolismus   MeSH
• hmotnostní spektrometrie metody   MeSH
• listy rostlin chemie   metabolismus   MeSH
• mastné kyseliny analýza   metabolismus   MeSH
• metabolomika metody   MeSH
• rezidua pesticidů analýza   MeSH
• Vitis chemie   metabolismus   MeSH
• vysokoúčinná kapalinová chromatografie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• fenoly MeSH
• flavonoidy MeSH
• mastné kyseliny MeSH
• rezidua pesticidů MeSH

Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.

• MeSH
• fenoly chemie   MeSH
• internet MeSH
• molekulární modely * MeSH
• molekulární struktura MeSH
• nikotinové receptory chemie   MeSH
• protein X asociovaný s bcl-2 chemie   MeSH
• software * MeSH
• statická elektřina MeSH
• vodík chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fenoly MeSH
• nikotinové receptory MeSH
• protein X asociovaný s bcl-2 MeSH
• vodík MeSH

Here, we report the data visualization, analysis and modeling for a large set of 4830 SN 2 reactions the rate constant of which (logk) was measured at different experimental conditions (solvent, temperature). The reactions were encoded by one single molecular graph - Condensed Graph of Reactions, which allowed us to use conventional chemoinformatics techniques developed for individual molecules. Thus, Matched Reaction Pairs approach was suggested and used for the analyses of substituents effects on the substrates and nucleophiles reactivity. The data were visualized with the help of the Generative Topographic Mapping approach. Consensus Support Vector Regression (SVR) model for the rate constant was prepared. Unbiased estimation of the model's performance was made in cross-validation on reactions measured on unique structural transformations. The model's performance in cross-validation (RMSE=0.61 logk units) and on the external test set (RMSE=0.80) is close to the noise in data. Performances of the local models obtained for selected subsets of reactions proceeding in particular solvents or with particular type of nucleophiles were similar to that of the model built on the entire set. Finally, four different definitions of model's applicability domains for reactions were examined.

• Klíčová slova
• Condensed Graph of Reaction, Generative Topographic Mapping, Matched Reaction Pairs, Support Vector Regression, bimolecular nucleophilic substitution reactions, models applicability domain,
• MeSH
• chemické modely * MeSH
• cyklické uhlovodíky chemie   MeSH
• kinetika MeSH
• oxidace-redukce MeSH
• support vector machine * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cyklické uhlovodíky MeSH

The investigation into human butyrylcholinesterase (hBChE) inhibitors as therapeutic agents for Alzheimer's disease (AD) holds significant promise, addressing both symptomatic relief and disease progression. In the pursuit of novel drug candidates with a selective BChE inhibition pattern, we focused on naturally occurring template structures, specifically Amaryllidaceae alkaloids of the carltonine-type. Herein, we explored a series of compounds implementing an innovative chemical scaffold built on the 3- and 4-benzyloxy-benzylamino chemotype. Notably, compounds 28 (hBChE IC50 = 0.171 ± 0.063 μM) and 33 (hBChE IC50 = 0.167 ± 0.018 μM) emerged as top-ranked hBChE inhibitors. In silico simulations elucidated the binding modes of these compounds within hBChE. CNS availability was predicted using the BBB score algorithm, corroborated by in vitro permeability assessments with the most potent derivatives. Compound 33 was also inspected for aqueous solubility, microsomal and plasma stability. Chemoinformatics analysis validated these hBChE inhibitors for oral administration, indicating favorable gastrointestinal absorption in compliance with Lipinski's and Veber's rules. Safety assessments, crucial for the chronic administration typical in AD treatment, were conducted through cytotoxicity testing on human neuroblastoma (SH-SY5Y) and hepatocellular carcinoma (HepG2) cell lines.

• Publikační typ
• časopisecké články MeSH