proteomics, metabolomics, protein glycation, diabites, biomarkers, carbonyl compounds, mass spectrometry
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Scopus Publications
Scopus Publications
Isolation, RP-UHPLC-ESI-LIT-Orbitrap-MS/MS-Based Metabolic Profiling and Anticandidal Activity of the Root and Leaf Secondary Metabolites of Monotes Kerstingii Gilg (Dipterocarpaceae) Sorelle Kache Fotsing, Dominique Ngnintedo, Yanick Kevin Dongmo Melogmo, Alena Soboleva, Kevine Dongmo Jumeta, et al. Chemistry and Biodiversity, 2026 The anticandidal activity of Monotes kerstingii leaf and root crude extracts was evaluated against five clinical Candida isolates: C. albicans , C. parapsilosis , C. krusei , C. glabrata and C. tropicalis . Extracts from both organs displayed Minimal Inhibitory Concentrations (MICs) ranging from 3.9 to 2000 µg/mL. Out of the five Candida species, the leaf hydroethanolic extract (EMKL) was the most active with MIC values of 3.9, 15.6 and 31.5 µg/mL on C. krusei, C. parapsilosis and C. albicans , respectively. The chemical investigation of these extracts led to the characterization of six previously undescribed metabolites, including a glycosylated stilbene: kerstingioside ( 1 ), three cis stilbene‐coumarins: cis ‐kerstilbcoumarin A–C ( 2–4 ) among which two as inseparable cis / trans ‐mixtures, one flavanone: kerstingiiflavanone ( 5 ) and one fatty acid glycoside, monestoside B ( 6 ), alongside with 22 known compounds. The distribution of the annotated metabolites in the roots and leaves was confirmed by comprehensive RP‐UHPLC‐Orbitrap‐MS and MS/MS analysis. In addition, all the isolated compounds were screened for their anticandidal activity. Stilbene 7 was the most active constituent, with MICs of 7.8, 15.6, and 15.6 µg/mL against C. albicans , C. krusei , and C. parapsilosis , respectively, while compounds 14 and 15 exhibited only moderate activity.
Metabolic Responses to the Zinc Stress in the Roots and Leaves of Amaranthus caudatus: The Proteomics View Anastasia Gurina, Tatiana Bilova, Daria Gorbach, Alena Soboleva, Nataliia Stepanova, et al. Plants, 2025 Zinc excess (Zn stress) could lead to deleterious effects in plants such as enhanced ROS production, inhibition of photosynthetic machinery, and impairment of nutrient uptake. Hence, we aimed to investigate the complexity of metabolic responses to Zn stress in Amaranthus caudatus young and mature leaves, as well as in roots by means of proteomics. Our previous metabolomics research has indicated potential involvement of gluconate and salicylate in Zn tolerance mechanisms. However, proteomics study of metabolic adjustments underlying Zn stress tolerance can give additional insight to the issue, as a lot of enzymes are known to be affected by the excess of transitional metals. The results obtained through bottom-up proteomics were complementary to our earlier metabolomics data and, furthermore, enlightened other important details in the metabolic response of A. caudatus plants to the applied Zn stress. In particular, the significant involvement of redox-related enzymes was shown, especially for the roots, and their possible interactions with salicylate and jasmonate signaling could be proposed. Furthermore, Zn2+-induced changes in roots and young leaves strongly affected sugar metabolism, enhanced protein quality control system, while mature leaves were characterized by remarkable decrease in subunits of photosynthetic electron transport complexes. Thus, this work emphasizes massive metabolic reprogramming aimed to reinforce root defense responses while supporting young leaves with sugar metabolites. Mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD069557.
Biological Potential of Methanol Extracts from Plants of the Genus Spiraea Spreading in Russia Anastasia Orlova, Alena Soboleva, Elena Tsvetkova, Svetlana Silinskaia, Yana L. Esaulkova, et al. International Journal of Molecular Sciences, 2025 The genus Spiraea is well represented in the Russian flora. Several phytochemical and bioactivity studies, completed so far with several individual species of this genus, indicate young Spiraea shoots as a promising source of pharmaceutically and nutraceutically active natural products. Therefore, a broad-scale phytochemical analysis of shoot extracts from multiple Russian Spiraea species (i.e., profiling of secondary metabolites and assignment of their structures), complemented with comprehensive activity screening, might give access to valuable information on the structure–activity relationship (SAR) of their constituents. However, despite a lot of phytochemical and bioactivity information on individual species being available, these data are mostly fragmentary and do not allow for building a general picture, and in-depth comprehensive studies are still missing. Therefore, to fill this gap, here, we present a comprehensive metabolite profiling study accomplished with 15 of the most widely spread Russian Spiraea species, which was complemented with appropriate bioactivity screening of their first-year shoot alcoholic extracts. A chromatography–mass spectrometric (LC-MS) analysis revealed 33 major constituents of the shoot isolates, which were dominated by flavonoids (quercetin and kaempferol derivatives) and hydroxycinnamic acids (caffeic, ferulic, and coumaric acid derivatives). Their relative quantification indicated that most of the identified major components were distributed among all of the studied extracts with minimal overlap in their composition and relative abundance. The antioxidant activity screening revealed the high efficiency of all of the extracts as potential redox protectors, acting at the levels of radical scavenging (DPPH assay) and quenching cation radicals (TEAC assay) and superoxide anion radicals (NBT assay). Screening the antiviral and antimicrobial activity of the same extracts revealed significant antiviral activity at a concentration of 2 µg/mL, and high (MIC < 1 mg/mL) or moderate (1 mg/mL ≤ MIC ≤ 4 mg/mL) antibacterial activity against Gram-positive and Gram-negative strains. The structures responsible for the manifestation of the studied types of activity were tentatively assigned using a bioinformatics-based strategy. This analysis revealed the most bioactive Spiraea species that might be promising for further in-depth phytochemical analysis and evaluations of their structure–activity relationships (SARs). In this context, we consider S. humilis, which simultaneously showed antioxidant, antimicrobial, and antiviral activity; S. media, with marked antioxidant, antimicrobial, and cytotoxic properties; S. ussuriensis, a strong antioxidant and cytotoxic species; and S. trilobata, with a combination of antioxidant and antiviral properties.
Investigation of CIP quality in over-the-counter drug stores of resource-limited countries: A comparative study in Vietnam and Nigeria Tran Nguyen Minh Thu, Itunuoluwa Celestina Oyelayo, Alexa Purgreth, Thi Thanh Xuan Ngo, Adekunle Olugbenga Olowe, et al. Jac Antimicrobial Resistance, 2025 Introduction CIP, a broad-spectrum antibiotic, is crucial for managing bacterial infections. Its efficacy relies on maintaining high-quality standards, which can be affected by manufacturing, regulatory oversight and storage practices. This study compares the quality of CIP preparations in Vietnam and Nigeria, two nations with contrasting regulatory frameworks, to assess compliance with pharmaceutical standards and identify risks from substandard or falsified medicines. Methods A total of 46 CIP preparations were analysed, 20 purchased from 13 vendors in Vietnam and 26 from 13 vendors in Nigeria. Data on vendor qualifications and storage conditions were collected. Antibacterial activity was tested using a modified disk diffusion assay, and content and purity were evaluated via reversed-phase HPLC. Results Vietnam's drug outlets showed stricter regulation, with 100% registration and 61.5% staffed by Bachelor of Pharmacy holders, compared with only 23.1% in Nigeria. Temperature and humidity monitoring was universal in Vietnam but minimal in Nigeria (23.1% and 15.4%, respectively). Antimicrobial testing confirmed effectiveness for all but one sample (Vietnam), while Nigerian samples had greater variability. Reversed-phase HPLC revealed seven Nigerian samples (26.9%) with &lt;80% declared CIP content, all from one manufacturer. Median content was 91% in Vietnam and 88% in Nigeria, with most samples meeting purity standards. Conclusions The study highlights significant disparities in the regulation, storage practices and quality of CIP between Vietnam and Nigeria. These findings underscore the critical need for improved regulation, monitoring and enforcement in countries with weaker pharmaceutical oversight to ensure drug efficacy and safety.
Strain-Specific Features of Primary Metabolome Characteristic for Extremotolerant/Extremophilic Cyanobacteria Under Long-Term Storage Tatiana Bilova, Nikita Golushko, Nadezhda Frolova, Alena Soboleva, Svetlana Silinskaia, et al. International Journal of Molecular Sciences, 2025 Cyanobacteria isolated from extreme habitats are promising in biotechnology due to their high adaptability to unfavorable environments and their specific natural products. Therefore, these organisms are stored under a reduced light supply in multiple collections worldwide. However, it remains unclear whether these strains maintain constitutively expressed primary metabolome features associated with their unique adaptations. To address this question, a comparative analysis of primary metabolomes of twelve cyanobacterial strains from diverse extreme habitats was performed by a combined GC-MS/LC-MS approach. The results revealed that all these cyanobacterial strains exhibited clear differences in their patterns of primary metabolites. These metabolic differences were more pronounced for the strains originating from ecologically different extreme environments. Extremotolerant terrestrial and freshwater strains contained lower strain-specifically accumulated primary metabolites than extremophilic species from habitats with high salinity and alkalinity. The latter group of strains was highly diverse in amounts of specific primary metabolites. This might indicate essentially different molecular mechanisms and metabolic pathways behind the survival of the microorganisms in saline and alkaline environments. The identified strain-specific metabolites are discussed with respect to the metabolic processes that might impact maintaining the viability of cyanobacteria during their storage and indicate unique adaptations formed in their original extreme habitats.
Responsivity of Two Pea Genotypes to the Symbiosis with Rhizobia and Arbuscular Mycorrhiza Fungi—A Proteomics Aspect of the “Efficiency of Interactions with Beneficial Soil Microorganisms” Trait Andrej Frolov, Julia Shumilina, Sarah Etemadi Afshar, Valeria Mashkina, Ekaterina Rhomanovskaya, et al. International Journal of Molecular Sciences, 2025 It is well known that individual pea (Pisum sativum L.) cultivars differ in their symbiotic responsivity. This trait is typically manifested with an increase in seed weights, due to inoculation with rhizobial bacteria and arbuscular mycorrhizal fungi. The aim of this study was to characterize alterations in the root proteome of highly responsive pea genotype k-8274 plants and low responsive genotype k-3358 ones grown in non-sterile soil, which were associated with root colonization with rhizobial bacteria and arbuscular mycorrhizal fungi (in comparison to proteome shifts caused by soil supplementation with mineral nitrogen salts). Our results clearly indicate that supplementation of the soil with mineral nitrogen-containing salts switched the root proteome of both genotypes to assimilation of the available nitrogen, whereas the processes associated with nitrogen fixation were suppressed. Surprisingly, inoculation with rhizobial bacteria had only a minor effect on the root proteomes of both genotypes. The most pronounced response was observed for the highly responsive k-8274 genotype inoculated simultaneously with rhizobial bacteria and arbuscular mycorrhizal fungi. This response involved activation of the proteins related to redox metabolism and suppression of excessive nodule formation. In turn, the low responsive genotype k-3358 demonstrated a pronounced inoculation-induced suppression of protein metabolism and enhanced diverse defense reactions in pea roots under the same soil conditions. The results of the study shed light on the molecular basis of differential symbiotic responsivity in different pea cultivars. The raw data are available in the PRIDE repository under the project accession number PXD058701 and project DOI 10.6019/PXD058701.
Green Light Drives Embryonic Photosynthesis and Protein Accumulation in Cotyledons of Developing Pea (Pisum sativum L.) Seeds Nataliia Stepanova, Elena Tarakhovskaya, Alena Soboleva, Anastasia Orlova, Aditi Basnet, et al. Agronomy, 2024 Photosynthesis is a vital process for seed productivity. It occurs in the leaves and provides developing seeds with the necessary nutrients. Moreover, many crops require photochemical reactions inside the seeds for proper development. The present study aimed to investigate Pisum sativum L. seeds at the middle stage of maturation, which is characterized by the active synthesis of nutrient reserves. Embryonic photosynthesis represents a crucial process to produce cells’ NADP(H) and ATP, which are necessary to convert sucrose into reserve biopolymers. However, it remains unclear how the pea embryo, covered by a coat and pericarp, receives sufficient light to provide energy for photochemical reactions. Recent studies have demonstrated that the photosynthetically active radiation reaching the developing pea embryo has a high proportion of green light. In addition, green light can be utilized in foliar photosynthesis by plants cultivated in shaded conditions. Here, we addressed the role of green light in seed development. Pea plants were cultivated under red and blue (RB) LEDs or red, green, and blue (RGB) LEDs. A Chl a fluorescence transient based on OJIP kinetics was detected at the periphery of the cotyledons isolated from developing seeds. Our findings showed that the addition of green light resulted in an increase in photochemical activity. Furthermore, the mature seeds that developed in the RGB module had a significantly higher weight and more storage proteins. Using a metabolomics approach, we also detected significant differences in the levels of organic acids, carbohydrates, nucleotide monophosphates, and nitrogenous substances between the RB and RGB conditions. Under RGB light, the cotyledons contained more ornithine, tryptophan, arginine, and aspartic acid. These changes indicate an impact of green light on the ornithine–urea cycle and polyamine biosynthesis. These results allow for a deeper understanding of the photochemical processes in embryos of developing seeds grown under a low light intensity. The photosynthetic system in the embryo cell adapts to the shade conditions by using green light.
The Effects of Selected Extraction Methods and Natural Deep Eutectic Solvents on the Recovery of Active Principles from Aralia elata var. mandshurica (Rupr. & Maxim.) J. Wen: A Non-Targeted Metabolomics Approach Alyona Kaleta, Nadezhda Frolova, Anastasia Orlova, Alena Soboleva, Natalia Osmolovskaya, et al. Pharmaceuticals, 2024 The methods and solvents employed in routine extraction protocols essentially impact the composition of the resulting extracts, i.e., the relative abundances of individual biologically active metabolites and the quality and stability of the isolates. Natural deep eutectic solvents (NADESs) represent a new class of environmentally friendly solvents, which are recognized as promising extractants alternative to conventional organic liquids. However, their relative efficiencies when applied in different extraction workflows are still poorly characterized. Therefore, here, we compare the potential of three extraction methods for the extraction of biologically active natural products from Aralia elata var. mandshurica with selected natural deep eutectic solvents (NADESs) using a non-targeted metabolomics approach. The non-targeted metabolite profiling relied on reversed-phase ultra-high-performance liquid chromatography–high-resolution mass spectrometry (RP-UHPLC-HR-MS). The roots of A. elata were extracted by maceration, ultrasound-assisted extraction (UAE), and vibrocavitation-assisted extraction (VAE). Principal component analysis (PCA) revealed a clear separation of the extracts obtained with the three extraction methods employed with NADES1 (choline chloride/malic acid) and NADES2 (sorbitol/malic acid/water). Based on the results of the hierarchical clustering analysis obtained for the normalized relative abundances of individual metabolites and further statistical evaluation with the t-test, it could be concluded that NADES1 showed superior extraction efficiency for all the protocols addressed. Therefore, this NADES was selected to compare the efficiencies of the three extraction methods in more detail. PCA followed by the t-test yielded only 3 metabolites that were more efficiently extracted by maceration, whereas 46 compounds were more abundant in the extracts obtained by VAE. When VAE and UAE were compared, 108 metabolites appeared to be more abundant in the extracts obtained by VAE, whereas only 1 metabolite was more efficiently recovered by UAE. These facts clearly indicate the advantage of the VAE method over maceration and UAE. Seven of the twenty-seven metabolites tentatively identified by tandem mass spectrometry (MS/MS) were found in the roots of A. elata for the first time. Additional studies are necessary to understand the applicability of VAE for the extraction of other plant materials.
Signaling in Legume–Rhizobia Symbiosis Julia Shumilina, Alena Soboleva, Evgeny Abakumov, Oksana Y. Shtark, Vladimir A. Zhukov, et al. International Journal of Molecular Sciences, 2023
