Objective: To study the cytotoxic effect of palmitic acid on myoblasts in vitro and the influence of this toxicant on the expression of myostatin mRNA in myoblast culture. Methods: To research the protective action against these processes of a compound with antioxidant activity, for which 2-ethyl-6-methyl-3-hydroxypyridine malate (ethoxidol) was chosen. Results: Our studies have shown that palmitic acid has a noticeable cytostatic effect on myoblasts in vitro, significantly suppressing their proliferation: the rate of MTT recovery in myoblasts treated with palmitate was only 9.6% of that rate in control myoblasts. In experiments, it was shown that palmitic acid slightly activated the expression of myostatin mRNA. At the same time, the protective effect of 2-ethyl-6-methyl-3-hydroxypyridine malate was not so pronounced. Conclusion: The results of our research indicate that the activation of myostatin synthesis is not one of the main causes of the development of myodystrophy in obese people or people following a high-lipid diet, while the direct cytotoxic effect of palmitic acid on myoblasts is. It is obvious that the use of antioxidants such as ethoxide has a protective effect on myoblasts in the experiment and may have a certain potential in clinical practice.

The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.

Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA-guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus providing defense from the phages. In addition, Cas13a-mediated tRNA cleavage indirectly activates the RNases of bacterial toxin-antitoxin modules cleaving messenger RNA, which could provide a backup defense. The mechanism of Cas13a-induced antiphage defense resembles that of bacterial anticodon nucleases, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module encompassing an anticodon nuclease.

Abstract Background. Acute myocardial infarction (AMI) represents a major cause of morbidity and mortality worldwide. Metabolomics investigation may be useful in the AMI pathogenesis research. Materials and methods. The article describes a comprehensive study of the AMI through the targeted metabolomic profiling. A total of 195 subjects were enrolled in the study, consisting of 68 AMI patients, 84 IHD patients and 43 non-CVD subjects. Metabolomic profiling was conducted, involving the quantitative analysis of 87 endogenous metabolites in plasma. Results. We identified 36 significantly changed metabolites in AMI, which included increased cystathionine and dimethylglycine and the decreased asymmetric dimethylarginine (ADMA) and arginine. It was found, that patients with AMI had significantly lower concentration of short chain acylcarnitines as compared to IHD and non-CVD patient. In patients with AMI concentration of xanthurenic acid and 3-OH-kynurenine was significantly decreased, as compared to IHD patients and non-CVD subjects. Norepinephrine was significantly decreased in patients with AMI and IHD, whereas its end-product – vanillylmandelic acid (VMA) – significantly increased. Based on the differences in the constructed weighted correlation networks, there were found new significant ratios of the metabolites. Among 23 established significantly altered metabolite ratios 14 ratios between non-CVD vs AMI and 17 ratios between IHD vs AMI were found. 9 ratios between non-CVD vs AMI and IHD vs AMI and 2 ratios between non-CVD vs IHD vs AMI were coincided. Conclusion. Obtained findings may pave the way for new insight of АMI pathogenesis and ultimately improving clinical outcomes.

Evaluation of the influence of primary and secondary aging on the manifestation of molecular and cellular hallmarks of aging is a challenging and currently unresolved issue. Our study represents the first demonstration of the distinct role of primary aging and chronic inflammation/physical inactivity - the most important drivers of secondary aging, in the regulation of transcriptomic and proteomic profiles in human skeletal muscle. To achieve this purpose, young healthy people (n = 15), young (n = 8) and older (n = 37) patients with knee/hip osteoarthritis, a model to study the effect of long-term inactivity and chronic inflammation on the vastus lateralis muscle, were included in the study. It was revealed that widespread and substantial age-related changes in gene expression in older patients relative to young healthy people (~4000 genes regulating mitochondrial function, proteostasis, cell membrane, secretory and immune response) were related to the long-term physical inactivity and chronic inflammation rather than primary aging. Primary aging contributed mainly to the regulation of genes (~200) encoding nuclear proteins (regulators of DNA repair, RNA processing, and transcription), mitochondrial proteins (genes encoding respiratory enzymes, mitochondrial complex assembly factors, regulators of cristae formation and mitochondrial reactive oxygen species production), as well as regulators of proteostasis. It was found that proteins associated with aging were regulated mainly at the post-transcriptional level. The set of putative primary aging genes and their potential transcriptional regulators can be used as a resource for further targeted studies investigating the role of individual genes and related transcription factors in the emergence of a senescent cell phenotype.

SCIENTIFIC RELEVANCE. In the quality control of proteolytic enzyme components of medicinal products, the activity of proteases is determined by spectrophotometry, which involves mea­suring the amidase or esterase activity using a synthetic substrate and the proteolytic activity using the Anson method. These methods require special substrates and have low sensitivity; their specificity may be insufficient, which may lead to serious errors. Quantitative mass spectrometry is an alternative approach to protease activity assays, which involves adding an isotope-labelled peptide to hydrolysates of the test enzyme. This approach allows determining the activity of proteases, notably, by the hydrolysis of specific peptide bonds, while simulta­neously confirming the identity and specificity of the test sample. Quantitative mass spectrometry has high sensitivity and does not require special substrates.AIM. This study aimed to investigate the possibility of enzymatic activity assay and enzyme identification by quantitative mass spectrometry with ¹⁸O labelling through an example of trypsin with casein.MATERIALS AND METHODS. The study used trypsin, casein, and H₂¹⁸O (Izotop, Russia). Peptide separation was performed using an Agilent 1100 HPLC system; mass spectra were obtained using a Bruker Ultraflex II MALDI-TOF/TOF mass spectrometer. Quantitative mass spectrometry was performed using a standard peptide, which was obtained from casein by tryptic digestion and HPLC purification. For ¹⁸O labelling, the authors dried the peptide and incubated it in H₂¹⁸О water. The quantitative analysis of the product was carried out using MALDI-TOF mass spectrometry. The authors used quantitative mass spectrometry with ¹⁸O labelling to determine enzymatic activity and calculate the Michaelis constant (KM).RESULTS. Following the tryptic digestion of casein, the authors identified the fragments corre­sponding to casein chains. The authors produced the isotope-labelled standard peptide and calculated its concentration using mass spectrometry. The authors determined the rate of casein digestion by trypsin and calculated the KM for trypsin, which was 13.65±0.60 μM. The standard deviation for repeated measurements showed that the mass-spectrometric method had a lower error of measurement than the spectrophotometric method. The sensitivity threshold for the mass-spectrometric method was 0.50±0.08 μM.CONCLUSIONS. The results obtained with trypsin confirm the possibility of enzymatic activity determination by the proposed method of quantitative mass spectrometry with ¹⁸O labelling. According to the sensitivity evaluation results, this method can be used for the simultaneous determination of enzyme activity, identity, and specificity. The proposed mass spectrometry approach is universal, it does not require expensive materials and reagents, and it can be easily adapted to determine the activity of virtually any protease.

Toxicity testing, including testing for skin toxicity, is essential for certification of novel pharmaceutical, chemical, and skincare products. The in vitro assessment models are considered to be the most promising; a number of such tests have been introduced into practice of approval testing. The new possibilities of detecting the early cellular response to damage can be provided by the cell-based sensors built upon visual quantification of the changes in activity of the signaling pathways involved in realization of such response. NF-κB and AP-1 represent two important protein transcription factors, the increase in activity of which in the cell is associated with damage, inflammation or redox balance alteration. The study was aimed to develop the cell-based sensors built upon the HaCaT immortalized human keratinocyte cell line that express green fluorescent protein (GFP) when the NF-κB (HaCaT/NF-κB) or AP-1 (HaCaT/AP-1) signaling pathway is activated, as well as to assess their information capacity when recording the dose-dependent response to the exposure to inducers of appropriate signaling pathways. The findings showed that the HaCaT/NF-κB cell fluorescence levels changed by 6.05 ± 0.51 and 5.53 ± 0.52 times upon exposure to TNFα or LPS (at a concentration of 0–80 ng/mL) in a dose dependent manner. The HaCaT/AP-1 biosensor also responded to the exposure to Cd (NO3)2 (at a concentration of 0–40 µМ) and ultraviolet A (UVA) (0–40 J/cm2), however, it enabled qualitative, but not quantitative detection. The censor cell fluorescence increased by 1.51 ± 0.24 and 1.66 ± 0.43 times, respectively. The cell-based sensors developed can be used to assess cytotoxic effects of the test substances on the human skin cells in vitro and study the cytotoxicity mechanisms.

Cardiovascular disease (CVD) represents one of the main causes of mortality worldwide and nearly a half of it is related to ischemic heart disease (IHD). The article represents a comprehensive study on the diagnostics of IHD through the targeted metabolomic profiling and machine learning techniques. A total of 112 subjects were enrolled in the study, consisting of 76 IHD patients and 36 non-CVD subjects. Metabolomic profiling was conducted, involving the quantitative analysis of 87 endogenous metabolites in plasma. A novel regression method of age-adjustment correction of metabolomics data was developed. We identified 36 significantly changed metabolites which included increased cystathionine and dimethylglycine and the decreased ADMA and arginine. Tryptophan catabolism pathways showed significant alterations with increased levels of serotonin, intermediates of the kynurenine pathway and decreased intermediates of indole pathway. Amino acid profiles indicated elevated branched-chain amino acids and increased amino acid ratios. Short-chain acylcarnitines were reduced, while long-chain acylcarnitines were elevated. Based on these metabolites data, machine learning algorithms: logistic regression, support vector machine, decision trees, random forest, and gradient boosting, were used for IHD diagnostic models. Random forest demonstrated the highest accuracy with an AUC of 0.98. The metabolites Norepinephrine; Xanthurenic acid; Anthranilic acid; Serotonin; C6-DC; C14-OH; C16; C16-OH; GSG; Phenylalanine and Methionine were found to be significant and may serve as a novel preliminary panel for IHD diagnostics. Further studies are needed to confirm these findings.

An increasing number of studies have investigated the effects of Cd on human health. Cd-induced dermatotoxicity is an important field of research, but numerous studies have focused on the effects of Cd on the human skin. Moreover, most studies have been performed using HaCaT cells but not primary keratinocytes. In this study, we provide the results describing the cytotoxic effects of Cd exposure on primary human epidermal keratinocytes obtained from different donors. The subtoxic concentration of cadmium chloride was determined via MTT assay, and transcriptomic analysis of the cells exposed to this concentration (25µM) was performed. As in HaCaT cells, Cd exposure resulted in increased ROS levels, cell cycle arrest, and induction of apoptosis. In addition, we report that exposure to Cd affects zinc and copper homeostasis, induces metallothionein expression, and activates various signaling pathways, including Nrf2, NF-kB, TRAIL, and PI3K. Cd induces the secretion of various cytokines (IL-1, IL-6, IL-10, and PGE2) and upregulates the expression of several cytokeratins, such as KRT6B, KRT6C, KRT16, and KRT17. The results provide a better understanding of the mechanisms of cadmium-induced cytotoxicity and its effect on human epidermal skin cells.