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Nature Communications Jun 2024Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a...
Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a few of the approximately 600 human E3 ligases are currently amenable to this strategy. This limits the actionable target space and clinical opportunities and thus establishes the necessity to expand to additional ligases. Here we identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12. SP3N features a minimal design, where a known FKBP12 ligand is appended with a flexible alkylamine tail that conveys degradation properties. We found that SP3N is a precursor and that the alkylamine is metabolized to an active aldehyde species that recruits the SCF ligase for FKBP12 degradation. Target engagement occurs via covalent adduction of Cys326 in the FBXO22 C-terminal domain, which is critical for ternary complex formation, ubiquitylation and degradation. This mechanism is conserved for two recently reported alkylamine-based degraders of NSD2 and XIAP, thus establishing alkylamine tethering and covalent hijacking of FBXO22 as a generalizable TPD strategy.
Topics: Humans; Proteolysis; Ubiquitination; F-Box Proteins; HEK293 Cells; Tacrolimus Binding Protein 1A; Ubiquitin-Protein Ligases; Amines; Proteasome Endopeptidase Complex; Ligands; Receptors, Cytoplasmic and Nuclear
PubMed: 38926334
DOI: 10.1038/s41467-024-49739-3 -
PloS One 2024Schistosomiasis is a neglected tropical disease which imposes a considerable and enduring impact on affected regions, leading to persistent morbidity, hindering child...
Schistosomiasis is a neglected tropical disease which imposes a considerable and enduring impact on affected regions, leading to persistent morbidity, hindering child development, diminishing productivity, and imposing economic burdens. Due to the emergence of drug resistance and limited management options, there is need to develop additional effective inhibitors for schistosomiasis. In view of this, quantitative structure-activity relationship studies, molecular docking, molecular dynamics simulations, drug-likeness and pharmacokinetics predictions were applied to 39 Schistosoma mansoni Thioredoxin Glutathione Reductase (SmTGR) inhibitors. The chosen QSAR model demonstrated robust statistical parameters, including an R2 of 0.798, R2adj of 0.767, Q2cv of 0.681, LOF of 0.930, R2test of 0.776, and cR2p of 0.746, confirming its reliability. The most active derivative (compound 40) was identified as a lead candidate for the development of new potential non-covalent inhibitors through ligand-based design. Subsequently, 12 novel compounds (40a-40l) were designed with enhanced anti-schistosomiasis activity and binding affinity. Molecular docking studies revealed strong and stable interactions, including hydrogen bonding, between the designed compounds and the target receptor. Molecular dynamics simulations over 100 nanoseconds and MM-PBSA free binding energy (ΔGbind) calculations validated the stability of the two best-designed molecules. Furthermore, drug-likeness and pharmacokinetics prediction analyses affirmed the potential of these designed compounds, suggesting their promise as innovative agents for the treatment of schistosomiasis.
Topics: Molecular Docking Simulation; Molecular Dynamics Simulation; Drug Design; Schistosoma mansoni; Ligands; Animals; Schistosomiasis; Quantitative Structure-Activity Relationship; NADH, NADPH Oxidoreductases; Humans; Multienzyme Complexes
PubMed: 38923997
DOI: 10.1371/journal.pone.0302390 -
Microbial Biotechnology Jun 2024Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss...
Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds.
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
Topics: Pseudomonas putida; Catabolite Repression; Pyruvate Dehydrogenase Complex; Hydrocarbons, Aromatic; Biodegradation, Environmental; Acetyl Coenzyme A; Pyruvic Acid; Gene Deletion; Metabolic Networks and Pathways
PubMed: 38923400
DOI: 10.1111/1751-7915.14514 -
Marine Drugs May 2024Acute myeloid leukemia (AML) is a hematologic malignancy characterized by infiltration of the blood and bone marrow, exhibiting a low remission rate and high recurrence...
Acute myeloid leukemia (AML) is a hematologic malignancy characterized by infiltration of the blood and bone marrow, exhibiting a low remission rate and high recurrence rate. Current research has demonstrated that class I HDAC inhibitors can downregulate anti-apoptotic proteins, leading to apoptosis of AML cells. In the present investigation, we conducted structural modifications of marine cytotoxin Santacruzamate A (SCA), a compound known for its inhibitory activity towards HDACs, resulting in the development of a novel series of potent class I HDACs hydrazide inhibitors. Representative hydrazide-based compound exhibited concentration-dependent induction of apoptosis in AML cells as a single agent. Moreover, exhibited a synergistic anti-AML effect when combined with Venetoclax, a clinical Bcl-2 inhibitor employed in AML therapy. This combination resulted in a more pronounced downregulation of anti-apoptotic proteins Mcl-1 and Bcl-xL, along with a significant upregulation of the pro-apoptotic protein cleaved-caspase3 and the DNA double-strand break biomarker γ-H2AX compared to monotherapy. These results highlighted the potential of as a promising lead compound for AML treatment, particularly when used in combination with Venetoclax.
Topics: Humans; Sulfonamides; Leukemia, Myeloid, Acute; Histone Deacetylase Inhibitors; Drug Synergism; Bridged Bicyclo Compounds, Heterocyclic; Apoptosis; Cell Line, Tumor; Antineoplastic Agents; Histone Deacetylase 1; Histone Deacetylases; Animals; Caspase 3; Myeloid Cell Leukemia Sequence 1 Protein
PubMed: 38921561
DOI: 10.3390/md22060250 -
Marine Drugs May 2024Cyanobacterial phycocyanin pigment is widely utilized for its properties in various industries, including food, cosmetics, and pharmaceuticals. Despite its potential,... (Comparative Study)
Comparative Study
Cyanobacterial phycocyanin pigment is widely utilized for its properties in various industries, including food, cosmetics, and pharmaceuticals. Despite its potential, challenges exist, such as extraction methods impacting yield, stability, and purity. This study investigates the impact of the number of freeze-thaw (FT) cycles on the extraction of phycocyanin from the wet biomass of four cyanobacteria species (, , sp., and sp.), along with the impact of five extraction solutions (Tris-HCl buffer, phosphate buffer, CaCl, deionized water, and tap water) at various pH values. sp. exhibited the highest phycocyanin content among the studied species. For , Tris-HCl buffer yielded maximum phycocyanin concentration from the first FT cycle, while phosphate buffer provided satisfactory results from the second cycle. Similarly, Tris-HCl buffer showed promising results for (68.5% of the maximum from the first cycle), with the highest concentration (~12% /) achieved during the seventh cycle, using phosphate buffer. sp. yielded the maximum pigment concentration from the first cycle using tap water. Among species-specific optimal extraction solutions, Tris-HCl buffer demonstrated sufficient extraction efficacy for all species, from the first cycle. This study represents an initial step toward establishing a universal extraction method for phycocyanin from diverse cyanobacteria species.
Topics: Phycocyanin; Cyanobacteria; Biomass; Solvents; Freezing; Hydrogen-Ion Concentration
PubMed: 38921557
DOI: 10.3390/md22060246 -
Genome Biology Jun 2024Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in multiple diseases. Increased glycolytic rates...
BACKGROUND
Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in multiple diseases. Increased glycolytic rates and lactate accumulation are associated with pathological angiogenesis.
RESULTS
Here, we show that a feedback loop between H3K9 lactylation (H3K9la) and histone deacetylase 2 (HDAC2) in endothelial cells drives VEGF-induced angiogenesis. We find that the H3K9la levels are upregulated in endothelial cells in response to VEGF stimulation. Pharmacological inhibition of glycolysis decreases H3K9 lactylation and attenuates neovascularization. CUT& Tag analysis reveals that H3K9la is enriched at the promoters of a set of angiogenic genes and promotes their transcription. Interestingly, we find that hyperlactylation of H3K9 inhibits expression of the lactylation eraser HDAC2, whereas overexpression of HDAC2 decreases H3K9 lactylation and suppresses angiogenesis.
CONCLUSIONS
Collectively, our study illustrates that H3K9la is important for VEGF-induced angiogenesis, and interruption of the H3K9la/HDAC2 feedback loop may represent a novel therapeutic method for treating pathological neovascularization.
Topics: Histone Deacetylase 2; Vascular Endothelial Growth Factor A; Histones; Feedback, Physiological; Humans; Animals; Neovascularization, Physiologic; Endothelial Cells; Mice; Human Umbilical Vein Endothelial Cells; Glycolysis; Neovascularization, Pathologic; Angiogenesis
PubMed: 38918851
DOI: 10.1186/s13059-024-03308-5 -
Asian Pacific Journal of Cancer... Jun 2024This study examined the morphological changes in the colonic mucosa and the presence of inflammation in rats induced with 1,2-dimethylhydrazine (DMH) 30 mg/kg BW over 9,...
OBJECTIVE
This study examined the morphological changes in the colonic mucosa and the presence of inflammation in rats induced with 1,2-dimethylhydrazine (DMH) 30 mg/kg BW over 9, 11, and 13 weeks without a latency period.
METHODS
Hematoxylin and eosin staining was performed to assess the morphology and characteristic alteration of the epitheliocytes in the colon. Immunohistochemistry was employed to assess the expression of tumor necrosis factor (TNF)-α and cyclooxygenase-2 (COX-2). The difference in the severity of inflammation and COX-2 expression was examined using one-way analysis of variance. The correlation of COX-2 expression with the severity of inflammation was analyzed using Spearman's rank correlation test.
RESULT
Until week 13, chronic inflammation and non-hyperplastic and hyperplastic aberrant crypt foci occurred. The severity of inflammation gradually shifted from high moderate to low moderate. TNF-α expression was high in all groups; however, COX-2 expression was gradually lower with longer duration of induction, which corresponded with the severity of inflammation.
CONCLUSION
DMH induction until week 13 without a latency period caused chronic inflammation without the formation of adenoma or adenocarcinoma. A very strong correlation was established between COX-2 expression and inflammation.
Topics: Animals; 1,2-Dimethylhydrazine; Rats; Colorectal Neoplasms; Cyclooxygenase 2; Inflammation; Male; Tumor Necrosis Factor-alpha; Intestinal Mucosa; Carcinogens; Rats, Sprague-Dawley; Aberrant Crypt Foci; Colon; Adenocarcinoma
PubMed: 38918668
DOI: 10.31557/APJCP.2024.25.6.2059 -
Nature Communications Jun 2024Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of...
Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.
Topics: Polyketides; Multigene Family; Polyketide Synthases; Mass Spectrometry; Data Mining; Machine Learning; Actinobacteria; Genome, Bacterial; Algorithms; Biological Products
PubMed: 38918378
DOI: 10.1038/s41467-024-49587-1 -
Plant Signaling & Behavior Dec 2024MYB transcription factor is one of the largest families in plants. There are more and more studies on plants responding to abiotic stress through MYB transcription...
MYB transcription factor is one of the largest families in plants. There are more and more studies on plants responding to abiotic stress through MYB transcription factors, but the mechanism of some family members responding to salt stress is unclear. In this study, physiological and transcriptome techniques were used to analyze the effects of the R2R3-MYB transcription factor on the growth and development, physiological function, and key gene response of . Phenotypic observation showed that the damage of overexpression strain was more serious than that of Col-0 after salt treatment, while the mutant strain showed less salt injury symptoms. Under salt stress, the decrease of chlorophyll content, the degree of photoinhibition of photosystem II (PSII) and photosystem I (PSI) and the degree of oxidative damage of overexpressed lines were significantly higher than those of Col-0. Transcriptome data showed that the number of differentially expressed genes (DEGs) induced by salt stress in overexpressed lines was significantly higher than that in Col-0. GO enrichment analysis showed that the response of to salt stress was mainly by affecting gene expression in cell wall ectoplast, photosystem I and photosystem II, and other biological processes related to photosynthesis. Compared with Col-0, the overexpression of under salt stress further inhibited the synthesis of chlorophyll a (Chla) and down-regulated most of the genes related to photosynthesis, which made the photosynthetic system more sensitive to salt stress. also caused the outbreak of reactive oxygen species and the accumulation of malondialdehyde under salt stress, which decreased the activity and gene expression of key enzymes in SOD, POD, and AsA-GSH cycle, thus destroying the ability of antioxidant system to maintain redox balance. negatively regulates the accumulation of osmotic regulatory substances such as soluble sugar (SS) and soluble protein (SP) in leaves under salt stress, which enhances the sensitivity of Arabidopsis leaves to salt. To sum up, negatively regulates the salt tolerance of by destroying the light energy capture, electron transport, and antioxidant capacity of Arabidopsis.
Topics: Arabidopsis; Photosynthesis; Plant Leaves; Arabidopsis Proteins; Salt Stress; Oxidative Stress; Gene Expression Regulation, Plant; Transcription Factors; Photosystem II Protein Complex; Photosystem I Protein Complex; Chlorophyll
PubMed: 38916149
DOI: 10.1080/15592324.2024.2371694 -
Scientific Reports Jun 2024Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is...
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
Topics: Animals; Male; Genome, Mitochondrial; Electron Transport Complex I; DNA, Mitochondrial; Female; Spermatozoa; Phylogeny; Open Reading Frames
PubMed: 38914611
DOI: 10.1038/s41598-024-63764-8