-
Database : the Journal of Biological... Jun 2024Drug transporters, integral membrane proteins found throughout the human body, play critical roles in physiological and biochemical processes through interactions with...
Drug transporters, integral membrane proteins found throughout the human body, play critical roles in physiological and biochemical processes through interactions with ligands, such as substrates and inhibitors. The extensive and disparate data on drug transporters complicate understanding their complex relationships with ligands. To address this challenge, it is essential to gather and summarize information on drug transporters, inhibitors and substrates, and simultaneously develop a comprehensive and user-friendly database. Current online resources often provide fragmented information and have limited coverage of drug transporter substrates and inhibitors, highlighting the need for a specialized, comprehensive and openly accessible database. ISTransbase addresses this gap by amassing a substantial amount of data from literature, government documents and open databases. It includes 16 528 inhibitors and 4465 substrates of 163 drug transporters from 18 different species, resulting in a total of 93 841 inhibitor records and 51 053 substrate records. ISTransbase provides detailed insights into drug transporters and their inhibitors/substrates, encompassing transporter and molecule structure, transporter function and distribution, as well as experimental methods and results from transport or inhibition experiments. Furthermore, ISTransbase offers three search strategies that allow users to retrieve drugs and transporters based on multiple selectable constraints, as well as perform checks for drug-drug interactions. Users can also browse and download data. In summary, ISTransbase (https://istransbase.scbdd.com/) serves as a valuable resource for accurately and efficiently accessing information on drug transporter inhibitors and substrates, aiding researchers in exploring drug transporter mechanisms and assisting clinicians in mitigating adverse drug reactions Database URL: https://istransbase.scbdd.com/.
Topics: Humans; Membrane Transport Proteins; Internet; Databases, Protein; Databases, Factual; Animals; Databases, Pharmaceutical
PubMed: 38943608
DOI: 10.1093/database/baae053 -
Molekuliarnaia Biologiia 2024Production of extracellular membrane vesicles plays an important role in communication in bacterial populations and in bacteria-host interactions. Vesicles as carriers...
Production of extracellular membrane vesicles plays an important role in communication in bacterial populations and in bacteria-host interactions. Vesicles as carriers of various regulatory and signaling molecules may be potentially used as disease biomarkers and promising therapeutic agents, including vaccine preparations. The composition of membrane vesicles has been deciphered for a limited number of Gram-negative and Gram-positive bacteria. In this work, for the first time, extracellular membrane vesicles of a streptomycin-resistant strain Bacillus pumilus 3-19, a producer of extracellular guanyl-preferring ribonuclease binase, are isolated, visualized, and characterized by their genome and proteome composition. It has been established that there is no genetic material in the vesicles and the spectrum of the proteins differs depending on the phosphate content in the culture medium of the strain. Vesicles from a phosphate-deficient medium carry 49 unique proteins in comparison with 101 from a medium with the high phosphate content. The two types of vesicles had 140 mutual proteins. Flagellar proteins, RNase J, which is the main enzyme of RNA degradosomes, phosphatases, peptidases, iron transporters, signal peptides, were identified in vesicles. Antibiotic resistance proteins and amyloid-like proteins whose genes are present in B. pumilus 3-19 cells are absent. Phosphate deficiency-induced binase was found only in vesicles from a phosphate-deficient medium.
Topics: Bacillus pumilus; Extracellular Vesicles; Proteome; Bacterial Proteins; Ribonucleases; Phosphates; Drug Resistance, Bacterial; Endoribonucleases
PubMed: 38943590
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Many viruses, including SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, enter host cells through a process of cell-viral membrane fusion that is...
Many viruses, including SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, enter host cells through a process of cell-viral membrane fusion that is activated by proteolytic enzymes. Typically, these enzymes are host cell proteases. Identifying the proteases that activate the virus is not a simple task but is important for the development of new antiviral drugs. In this study, we developed a bioinformatics method for identifying proteases that can cleave viral envelope glycoproteins. The proposed approach involves the use of predictive models for the substrate specificity of human proteases and the application of a structural analysis method for predicting the vulnerability of protein regions to proteolysis based on their 3D structures. Specificity models were constructed for 169 human proteases using information on their known substrates. A previously developed method for structural analysis of potential proteolysis sites was applied in parallel with specificity models. Validation of the proposed approach was performed on the SARS-CoV-2 spike protein, whose proteolysis sites have been well studied.
Topics: Spike Glycoprotein, Coronavirus; Humans; SARS-CoV-2; Computational Biology; Proteolysis; Substrate Specificity; Peptide Hydrolases; COVID-19; Pandemics; Models, Molecular; Betacoronavirus
PubMed: 38943589
DOI: No ID Found -
Molekuliarnaia Biologiia 2024CRISPR/Cas systems are perspective molecular tools for targeted manipulation with genetic materials, such as gene editing, regulation of gene transcription, modification...
CRISPR/Cas systems are perspective molecular tools for targeted manipulation with genetic materials, such as gene editing, regulation of gene transcription, modification of epigenome etc. While CRISPR/Cas systems proved to be highly effective for correcting genetic disorders and treating infectious diseases and cancers in experimental settings, clinical translation of these results is hampered by the lack of efficient CRISPR/Cas delivery vehicles. Modern synthetic nanovehicles based on organic and inorganic polymers have many disadvantages, including toxicity issues, the lack of targeted delivery, and complex and expensive production pipelines. In turn, exosomes are secreted biological nanoparticles that exhibit high biocompatibility, physico-chemical stability, and the ability to cross biological barriers. Early clinical trials found no toxicity associated with exosome injections. In the recent years, exosomes have been considered as perspective delivery vehicles for CRISPR/Cas systems in vivo. The aim of this study was to analyze the efficacy of CRISPR/Cas stochastic packaging into exosomes for several human cell lines. Here, we show that Cas9 protein is effectively localized into the compartment of intracellular exosome biogenesis, but stochastic packaging of Cas9 into exosomes turns to be very low (~1%). As such, stochastic packaging of Cas9 protein is very ineffective and cannot be used for gene editing purposes. Developing novel tools and technologies for loading CRISPR/Cas systems into exosomes is needed.
Topics: Exosomes; Humans; CRISPR-Cas Systems; Gene Editing; CRISPR-Associated Protein 9
PubMed: 38943588
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Streptococcus pyogenes Cas9 (SpCas9) is the most popular tool in gene editing; however, off-target mutagenesis is one of the biggest impediments in its application. In...
Streptococcus pyogenes Cas9 (SpCas9) is the most popular tool in gene editing; however, off-target mutagenesis is one of the biggest impediments in its application. In our previous study, we proposed the HH theory, which states that sgRNA/DNA hybrid (hybrid) extrusion-induced enhancement of hydrophobic interactions between the hybrid and REC3/HNH is a key factor in cleavage initiation. Based on the HH theory, we analyzed the interactions between the REC3 domain and hybrid and obtained 8 mutant sites. We designed 8 SpCas9 variants (V1-V8), used digital droplet PCR to assess SpCas9-induced DNA indels in human cells, and developed high-fidelity variants. Thus, the HH theory may be employed to further optimize SpCas9-mediated genome editing systems, and the resultant V3, V6, V7, and V8 SpCas9 variants may be valuable for applications requiring high-precision genome editing.
Topics: Humans; Gene Editing; CRISPR-Associated Protein 9; CRISPR-Cas Systems; Streptococcus pyogenes; HEK293 Cells; INDEL Mutation; RNA, Guide, CRISPR-Cas Systems; DNA
PubMed: 38943587
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Melatonin (N-acetyl-5-methoxytryptamine, MEL) is a hormone synthesized by the pineal gland. Due to its oncostatic effect, it can be considered as an antitumor agent and...
Melatonin (N-acetyl-5-methoxytryptamine, MEL) is a hormone synthesized by the pineal gland. Due to its oncostatic effect, it can be considered as an antitumor agent and used for combination therapy. ABT-737, a Bcl-2 inhibitor, promotes cell death after treatment with agents that induce pro-apoptotic signals. In the present study, the combined effect of MEL and ABT-737 on changes in proliferative and mitotic activity, mitochondrial membrane potential, intracellular production of reactive oxygen species (ROS), and cytosolic Ca^(2+) was studied. Moreover, changes in the expression of anti- and pro-apoptotic proteins (Bcl-2 and Bax), autophagy markers (LC3A/B (I, II)), endoplasmic reticulum stress markers (chaperones BIP and PDI, CHOP) were studied under these conditions. The effect of MEL together with ABT-737 led to an increase in the level of cytosolic Ca^(2+), intracellular production of ROS and a decrease in the membrane potential of mitochondria. The content of Bcl-2 increased, while the level of Bax decreased. Activation of CHOP stimulated autophagy and led to a decrease in the synthesis of chaperones BIP and PDI. It is assumed that melatonin can enhance the effect of other chemotherapeutic agents and can be used in the treatment of tumors.
Topics: Humans; Sulfonamides; Melatonin; Nitrophenols; Piperazines; Biphenyl Compounds; Reactive Oxygen Species; Membrane Potential, Mitochondrial; Apoptosis; Proto-Oncogene Proteins c-bcl-2; THP-1 Cells; bcl-2-Associated X Protein; Drug Synergism; Autophagy; Endoplasmic Reticulum Stress; Endoplasmic Reticulum Chaperone BiP; Cell Proliferation; Microtubule-Associated Proteins; Calcium; Neoplasm Proteins; Transcription Factor CHOP
PubMed: 38943585
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Current data on the molecular mechanisms of liver fibrosis and cirrhosis fail to fully explain all stages of their development. Interactions between individual genes and...
Current data on the molecular mechanisms of liver fibrosis and cirrhosis fail to fully explain all stages of their development. Interactions between individual genes and signaling pathways are known to play an important role in their functions. However, data on their relationships are insufficient and often contradictory. For the first time, mRNA expression of Notch1, Notch2, Yap1, Tweak (Tnfsf12), Fn14 (Tnfrsf12a), Ang, Vegfa, Cxcl12 (Sdf), Nos2, and Mmp-9 was studied in detail at several stages of thioacetamide-induced liver fibrosis in Wistar rats. A factor analysis isolated three factors, which combined highly correlated target genes. The first factor included four genes: Cxcl12 (r = 0.829, p < 0.05), Tweak (r = 0.841, p < 0.05), Notch1 (r = 0.848, p < 0.05), and Yap1 (r = 0.921, p < 0.05). The second factor described the correlation between Mmp-9 (r = 0.791, p < 0.05) and Notch2 (r = 0.836, p < 0.05). The third factor included Ang (r = 0.748, p < 0.05) and Vegfa (r = 0.679, p < 0.05). The Nos2 and Fn14 genes were not included in any of the factors. The gene grouping by mRNA expression levels made it possible to assume a pathogenetic relationship between their products in the development of fibrotic changes due to liver toxicity.
Topics: Animals; Rats; YAP-Signaling Proteins; Rats, Wistar; Male; Receptor, Notch1; RNA, Messenger; Chemokine CXCL12; Cytokine TWEAK; Matrix Metalloproteinase 9; Gene Expression Regulation; Liver Cirrhosis; Thioacetamide; Receptor, Notch2; Transcription Factors; Nitric Oxide Synthase Type II
PubMed: 38943584
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Regulation of retrotransposon activity in somatic tissues is a complex mechanism that has still not been studied in detail. It is strongly believed that siRNA...
Regulation of retrotransposon activity in somatic tissues is a complex mechanism that has still not been studied in detail. It is strongly believed that siRNA interference is main mechanism of retrotransposon activity regulation outside the gonads, but recently was demonstrated that piRNA interference participates in retrotransposon repression during somatic tissue development. In this work, using RT-PCR, we demonstrated that during ontogenesis piRNA interference determinates retrotransposon expression level on imago stage and retrotransposons demonstrate tissue-specific expression. The major factor of retrotransposon tissue-specific expression is presence of transcription factor binding sites in their regulatory regions.
Topics: Animals; Drosophila melanogaster; Retroelements; RNA, Small Interfering; Gene Expression Regulation, Developmental; Transcription Factors; Drosophila Proteins; Organ Specificity; Binding Sites; RNA Interference
PubMed: 38943583
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Stress can play a significant role in arterial hypertension and many other complications of cardiovascular diseases. Considerable attention is paid to the study of the...
Stress can play a significant role in arterial hypertension and many other complications of cardiovascular diseases. Considerable attention is paid to the study of the molecular mechanisms involved in the body response to stressful influences, but there are still many blank spots in understanding the details. ISIAH rats model the stress-sensitive form of arterial hypertension. ISIAH rats are characterized by genetically determined enhanced activities of the hypothalamic-pituitary-adrenocortical and sympathetic-adrenomedullary systems, suggesting a functional state of increased stress reactivity. For the first time, the temporal expression patterns of Fos and several related genes were studied in the hypothalamus of adult male hypertensive ISIAH rats after a single exposure to restraint stress for 30, 60, or 120 min. Fos transcription was activated and peaked 1 h after the start of restraint stress. The time course of Fos activation coincided with that of blood pressure increase after stress. Activation of hypothalamic neurons also alters the transcription levels of several transcription factor genes (Jun, Nr4a3, Jdp2, and Ppargc1a), which are associated with the development of cardiovascular diseases. Because Fos induction is a marker of brain neuron activation, activation of hypothalamic neurons and an increase in blood pressure were concluded to accompany increased stress reactivity of the hypothalamic-pituitary-adrenocortical and sympathoadrenal systems in hypertensive ISIAH rats during short-term restraint.
Topics: Animals; Hypertension; Rats; Hypothalamus; Male; Gene Expression Regulation; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha; Proto-Oncogene Proteins c-fos; Restraint, Physical; Stress, Psychological; Blood Pressure; Stress, Physiological; Neurons
PubMed: 38943581
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Spore-forming bacteria have a unique resistance to negative environmental conditions, including aggressive space factors, and are an excellent model for studying...
Spore-forming bacteria have a unique resistance to negative environmental conditions, including aggressive space factors, and are an excellent model for studying adaptation mechanisms and survival strategies at the molecular level. The study analyzed the genome of Bacillus velezensis, which remained viable after a 2-year exposure in outer space on the outer surface of the ISS as part of the Test space experiment. A comparative analysis of the draft genomes of the exhibit strain and the ground control did not reveal significant changes; the average nucleotide identity was 99.98%, which indicates the ability of microorganisms to maintain genome stability in space conditions, due to both increased stress resistance of bacterial spores and efficient operation of the system of repair of accumulated changes. The study of a single nucleotide polymorphism in the genome of B. velezensis revealed nine point substitutions, three of which are in intergenic regions, six in protein-coding genes, three of them are missense mutations, two nucleotide deletions leading to a shift in the reading frame, and one synonymous substitution. The profiles of the housekeeping genes were determined during MLST typing and it was found that the allelic profiles obtained for B. velezensis T15.2 and 924 strains do not correspond to any of the previously described sequence types. The presented results indicate the ability of B. velezensis bacteria to maintain the viability of spores and the integrity of the genome for a long time under extreme conditions of outer space, which is important for the problem of planetary protection, as well as the potential possibility of performing biotechnological processes based on B. velezensis during space exploration.
Topics: Bacillus; Genomic Instability; Genome, Bacterial; Polymorphism, Single Nucleotide; Spores, Bacterial; Multilocus Sequence Typing
PubMed: 38943579
DOI: No ID Found