Исследование in silico взаимодействия производных 2’-{[(e)-андрост-5-ен-17-илиден]-метил}оксазолинов с андрогеновым рецептором

The ability of novel oxazolinyl derivatives of pregna-5,17(20)-diene to interact with the androgen receptor (AR) was investigated using molecular modelling methods. Six new derivatives differed in oxazolinyl radicals in 17 position were used. It was shown that all compounds were able to docked in the ligand-binding domain of AR only when the AR helix-12 was removed. It is suggested that these compounds have antagonistic properties. Results of docking and simulation of molecular dynamics with estimation of binding energy allow to predict that two compounds can be effective AR antagonists.Методами молекулярного моделирования оценена способность новых азотсодержащих стероидных производных 2’-{[(E)-андрост-5-ен-17-илиден]-метил}оксазолинов взаимодействовать с андрогенным рецептором. Исследованы 6 оксазолиновых производных 17(20)Е-прегна-5,17(20)-диена, различающихся структурой гетероцикла. Показано, что все соединения способны связываться с андрогенным рецептором только в случае, когда из структуры рецептора была удалена 12 спираль. Это позволяет предполагать, что данные лиганды должны проявлять антагонистические свойства. Результаты докинга и молекулярной динамики с оценкой энергии связывания лигандов позволили предположить, что два из исследованных соединений могут быть эффективными антагонистами андрогенного рецептора

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors

As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro. By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance. © Copyright © 2020 Veselovsky, Dyachkova, Menyaylo, Polyaeva, Olekhnovich, Shitikov, Bespiatykh, Semashko, Kasianov, Ilina, Danilenko and Klimina

Toxin-antitoxin systems: A tool for taxonomic analysis of human intestinal microbiota

The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing theHGMat the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM. © 2020 by the authors

New steroidal oxazolines, benzoxazoles and benzimidazoles related to abiraterone and galeterone

Seven new oxazoline, benzoxazole and benzimidazole derivatives were synthesized from 3β-acetoxyandrosta-5,16-dien-17-carboxylic, 3β-acetoxyandrost-5-en-17β-carboxylic and 3β-acetoxypregn-5-en-21-oic acids. Docking to active site of human 17α-hydroxylase/17,20-lyase revealed that all oxazolines, as well as benzoxazoles and benzimidazoles comprising Δ16 could form stable complexes with enzyme, in which steroid moiety is positioned similarly to that of abiraterone and galeterone, and nitrogen atom coordinates heme iron, while 16,17-saturated benzoxazoles and benzimidazoles could only bind in a position where heterocycle is located nearly parallel to heme plane. Modeling of the interaction of new benzoxazole and benzimidazole derivatives with androgen receptor revealed the destabilization of helix 12, constituting activation function 2 (AF2) site, by mentioned compounds, similar to one induced by known antagonist galeterone. The synthesized compounds inhibited growth of prostate carcinoma LNCaP and PC-3 cells at 96 h incubation; the potency of 2′-(3β-hydroxyandrosta-5,16-dien-17-yl)-4′,5′-dihydro-1′,3′-oxazole and 2′-(3β-hydroxyandrosta-5,16-dien-17-yl)-benzimidazole was superior and could inspire further investigations of these compounds as potential anti-cancer agents. © 2019 Elsevier Inc

An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform

Abstract Background Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms. Results We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run. Conclusions The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors

As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro. By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance. © Copyright © 2020 Veselovsky, Dyachkova, Menyaylo, Polyaeva, Olekhnovich, Shitikov, Bespiatykh, Semashko, Kasianov, Ilina, Danilenko and Klimina