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Search Results (452)

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Keywords = pyrimidin-4(3H)-one

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20 pages, 15855 KiB  
Article
Resistance Response and Regulatory Mechanisms of Ciprofloxacin-Induced Resistant Salmonella Typhimurium Based on Comprehensive Transcriptomic and Metabolomic Analysis
by Xiaohan Yang, Jinhua Chu, Lulu Huang, Muhammad Haris Raza Farhan, Mengyao Feng, Jiapeng Bai, Bangjuan Wang and Guyue Cheng
Antibiotics 2025, 14(8), 767; https://doi.org/10.3390/antibiotics14080767 - 29 Jul 2025
Viewed by 298
Abstract
Background: Salmonella infections pose a serious threat to both animal and human health worldwide. Notably, there is an increasing trend in the resistance of Salmonella to fluoroquinolones, the first-line drugs for clinical treatment. Methods: Utilizing Salmonella Typhimurium CICC 10420 as the test strain, [...] Read more.
Background: Salmonella infections pose a serious threat to both animal and human health worldwide. Notably, there is an increasing trend in the resistance of Salmonella to fluoroquinolones, the first-line drugs for clinical treatment. Methods: Utilizing Salmonella Typhimurium CICC 10420 as the test strain, ciprofloxacin was used for in vitro induction to develop the drug-resistant strain H1. Changes in the minimum inhibitory concentrations (MICs) of various antimicrobial agents were determined using the broth microdilution method. Transcriptomic and metabolomic analyses were conducted to investigate alterations in gene and metabolite expression. A combined drug susceptibility test was performed to evaluate the potential of exogenous metabolites to restore antibiotic susceptibility. Results: The MICs of strain H1 for ofloxacin and enrofloxacin increased by 128- and 256-fold, respectively, and the strain also exhibited resistance to ceftriaxone, ampicillin, and tetracycline. A single-point mutation of Glu469Asp in the GyrB was detected in strain H1. Integrated multi-omics analysis showed significant differences in gene and metabolite expression across multiple pathways, including two-component systems, ABC transporters, pentose phosphate pathway, purine metabolism, glyoxylate and dicarboxylate metabolism, amino sugar and nucleotide sugar metabolism, pantothenate and coenzyme A biosynthesis, pyrimidine metabolism, arginine and proline biosynthesis, and glutathione metabolism. Notably, the addition of exogenous glutamine, in combination with tetracycline, significantly reduced the resistance of strain H1 to tetracycline. Conclusion: Ciprofloxacin-induced Salmonella resistance involves both target site mutations and extensive reprogramming of the metabolic network. Exogenous metabolite supplementation presents a promising strategy for reversing resistance and enhancing antibiotic efficacy. Full article
(This article belongs to the Section Mechanism and Evolution of Antibiotic Resistance)
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13 pages, 1147 KiB  
Hypothesis
Possible Enantioseparation of Racemic Ribose on Chiral Surface Formed by Adsorption of Nucleobases
by Roman Bielski and Michal Tencer
Life 2025, 15(8), 1160; https://doi.org/10.3390/life15081160 - 23 Jul 2025
Viewed by 248
Abstract
The paper proposes a putative prebiotic scenario leading to homochirality in the RNA world. In this scenario, racemic ribose, the only chiral moiety in RNA, was enantioseparated (in its pyranose form) on a chiral surface formed by the adsorption of (prochiral) nucleobases (NBs) [...] Read more.
The paper proposes a putative prebiotic scenario leading to homochirality in the RNA world. In this scenario, racemic ribose, the only chiral moiety in RNA, was enantioseparated (in its pyranose form) on a chiral surface formed by the adsorption of (prochiral) nucleobases (NBs) on a mineral or metal. Purine bases (adenine and guanine) are more likely candidates for this process than pyrimidine bases because they have more H-bond donors and acceptors. Another possible candidate surface for the enantioseparation of ribose would be formed by the adsorption of nucleobase pairs, e.g., guanine–cytosine (GC). Interactions of ribose molecules with hydrogen bond donors and acceptors of NBs or NB pairs (located on the surface) enforced the orientation of ribose molecules in two directions perpendicular to each other and parallel to the surface. Consequently, the energy of interactions of enantiomers of the sugar with the surface was not the same. Thus, a solvent moving along the surface caused the enantiomers of ribose to move with different rates, resulting in the enantioseparation of ribose in a chromatography-like process. The same process would also separate ribose from other monosaccharides in the mix. Hydrogen bonding between nucleobases was also pivotal in the formation of large homochiral domains on the surfaces. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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19 pages, 4720 KiB  
Review
Changes in Thermodynamic Parameters Induced by Pyrimidine Nucleic Bases Forming Complexes with Amino Acids and Peptides in a Buffer Solution at pH = 7.4
by Elena Yu. Tyunina, Vladimir P. Barannikov and Igor N. Mezhevoi
Liquids 2025, 5(3), 19; https://doi.org/10.3390/liquids5030019 - 22 Jul 2025
Viewed by 194
Abstract
This article presents a mini-review of the available data on the thermodynamics of the complexation of amino acids and peptides with some nucleic bases in a buffer medium. Data on changes in thermodynamic parameters (binding constants, Gibbs energy, enthalpy, entropy) during the complexation [...] Read more.
This article presents a mini-review of the available data on the thermodynamics of the complexation of amino acids and peptides with some nucleic bases in a buffer medium. Data on changes in thermodynamic parameters (binding constants, Gibbs energy, enthalpy, entropy) during the complexation of nucleic bases with amino acids and peptides as a function of physicochemical properties are given at T = 298.15 K. The effects of complexation on the volumetric properties of nucleic bases, including apparent molar volumes, standard molar volumes, and limiting molar expansibility, over a temperature range of 288.15 to 313.15 K are considered in detail. Differences in the behavior of amino acids and peptides caused by different modes of coordination with nucleic bases are noted. These manifest in the stoichiometry of the formed complexes, the relationship with the acid dissociation constants of carboxyl and amino groups, enthalpy–entropy compensation in the complexation process, the temperature dependence of the transfer volumes, and the effect of hydrophobicity on volumetric characteristics. Full article
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14 pages, 1649 KiB  
Article
LC-MS-Based Untargeted Metabolic Profiling in Plasma Following Dapagliflozin Administration in Healthy Volunteers
by Hyeon Ji Kim, Jae Hwa Lee, Ji Seo Park, Jin Ju Park, Hae Won Lee, Heeyoun Bunch, Sook Jin Seong, Mi-Ri Gwon and Young-Ran Yoon
Metabolites 2025, 15(7), 484; https://doi.org/10.3390/metabo15070484 - 17 Jul 2025
Viewed by 474
Abstract
Dapagliflozin, a sodium-glucose cotransporter 2 inhibitor, treats type 2 diabetes by blocking renal glucose reabsorption and promoting urinary glucose excretion. This mechanism lowers blood glucose concentrations independently of insulin. The resulting caloric loss also contributes to weight reduction. Although these effects are well [...] Read more.
Dapagliflozin, a sodium-glucose cotransporter 2 inhibitor, treats type 2 diabetes by blocking renal glucose reabsorption and promoting urinary glucose excretion. This mechanism lowers blood glucose concentrations independently of insulin. The resulting caloric loss also contributes to weight reduction. Although these effects are well documented in patients with diabetes, their magnitude and underlying mechanisms in healthy individuals remain poorly understood. Background/Objectives: We investigated metabolic alterations after a single 10 mg dose of dapagliflozin in healthy adults with normal body-mass indices (BMIs) using untargeted metabolomics. Methods: Thirteen healthy volunteers completed this study. Plasma was collected before and 24 h after dosing. Untargeted metabolic profiling was performed with ultra-high-performance liquid chromatography–quadrupole time-of-flight/mass spectrometry. Results: Twenty-five endogenous metabolites were annotated; ten were putatively identified. Eight metabolites increased significantly, whereas two decreased. Up-regulated metabolites included phosphatidylcholine (PC) species (PC O-36:5, PC 36:3), phosphatidylserine (PS) species (PS 40:2, PS 40:3, PS 36:1, PS 40:4), lysophosphatidylserine 22:1, and uridine. Dehydroepiandrosterone sulfate and bilirubin were down-regulated. According to the Human Metabolome Database, these metabolites participate in glycerophospholipid, branched-chain amino acid, pyrimidine, and steroid-hormone metabolism. Conclusions: Dapagliflozin may affect pathways related to energy metabolism and homeostasis beyond glucose regulation. These data provide a reference for future investigations into energy balance and metabolic flexibility in metabolic disorders. Full article
(This article belongs to the Section Pharmacology and Drug Metabolism)
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20 pages, 2020 KiB  
Article
Diastereoselective Synthesis and Biological Evaluation of Spiro[chromane-2,4′-pyrimidin]-2′(3′H)-ones as Novel Antimicrobial and Antioxidant Agents
by Alena S. Karandeeva, Natalia A. Bogdanova, Mariya V. Kabanova, Sergey I. Filimonov, Zhanna V. Chirkova, Anna A. Romanycheva, Valeria A. Panova, Anton A. Shetnev, Nurila A. Togyzbayeva, Saken A. Kanzhar, Nurbol O. Appazov and Kyrill Yu. Suponitsky
Molecules 2025, 30(14), 2954; https://doi.org/10.3390/molecules30142954 - 14 Jul 2025
Viewed by 626
Abstract
This study reports an improved diastereoselective synthesis of substituted spiro[chromane-2,4′-pyrimidin]-2′(3′H)-ones via the acid-catalyzed condensation of 6-styryl-4-aryldihydropyrimidin-2-ones with resorcinol, 2-methylresorcinol, and pyrogallol. The optimized method allows for the isolation of diastereomerically pure products, with stereoselectivity controlled by varying acid catalysts (e.g., methanesulfonic [...] Read more.
This study reports an improved diastereoselective synthesis of substituted spiro[chromane-2,4′-pyrimidin]-2′(3′H)-ones via the acid-catalyzed condensation of 6-styryl-4-aryldihydropyrimidin-2-ones with resorcinol, 2-methylresorcinol, and pyrogallol. The optimized method allows for the isolation of diastereomerically pure products, with stereoselectivity controlled by varying acid catalysts (e.g., methanesulfonic acid vs. toluenesulfonic acid) and solvent conditions. The synthesized compounds were evaluated for antimicrobial and antioxidant activities. Notably, the (2S*,4R*,6′R*)-diastereomers exhibited significant antibacterial activity against both Gram-positive and Gram-negative bacterial strains with minimal inhibition concentration down to 2 µg/mL, while derivatives containing vicinal bisphenol moieties demonstrated potent antioxidant activity, with IC50 values (12.5 µg/mL) comparable to ascorbic acid. Pharmacokinetic analysis of selected hit compounds revealed favorable drug-like properties, including high gastrointestinal absorption and blood-brain barrier permeability. These findings highlight the potential of spirochromane-pyrimidine hybrids as promising candidates for further development in the treatment of infectious diseases and oxidative stress-related pathologies. Full article
(This article belongs to the Special Issue Design, Synthesis and Applications of Bioactive Compounds)
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14 pages, 1523 KiB  
Article
Foliar Nitrogen Application Enhances Nitrogen Assimilation and Modulates Gene Expression in Spring Wheat Leaves
by Yanlin Yao, Wenyan Ma, Xin Jin, Guangrui Liu, Yun Li, Baolong Liu and Dong Cao
Agronomy 2025, 15(7), 1688; https://doi.org/10.3390/agronomy15071688 - 12 Jul 2025
Viewed by 249
Abstract
Nitrogen (N) critically regulates wheat growth and grain quality, yet the molecular mechanisms underlying foliar nitrogen application remain unclear. This study evaluated the effects of foliar nitrogen application (12.25 kg ha−1) on the growth, grain yield, and quality of spring wheat, [...] Read more.
Nitrogen (N) critically regulates wheat growth and grain quality, yet the molecular mechanisms underlying foliar nitrogen application remain unclear. This study evaluated the effects of foliar nitrogen application (12.25 kg ha−1) on the growth, grain yield, and quality of spring wheat, as well as its molecular mechanisms. The results indicated that N was absorbed within 3 h post-application, with leaf nitrogen concentration peaking at 12 h. The N treatment increased whole-plant dry matter accumulation and grain protein content by 11.34% and 6.8%, respectively. Amino acid content peaked 24 h post-application, increasing by 25.3% compared to the control. RNA-sequencing analysis identified 4559 and 3455 differentially expressed genes at 3 h and 24 h after urea treatment, respectively, these DEGs being primarily involved in nitrogen metabolism, photosynthetic carbon fixation, amino acid biosynthesis, antioxidant systems, and nucleotide biosynthesis. Notably, the plastidic glutamine synthetase gene (GS2) is crucial in the initial phase of urea application (3 h post-treatment). The pronounced downregulation of GS2 initiates a reconfiguration of nitrogen assimilation pathways. This downregulation impedes glutamine synthesis, resulting in a transient accumulation of free ammonia. In response to ammonia toxicity, the leaves promptly activate the GDH (glutamate dehydrogenase) pathway to facilitate the temporary translocation of ammonium. This compensatory mechanism suggests that GS2 downregulation may be a key switch that redirects nitrogen metabolism from the GS/GOGAT cycle to the GDH bypass. Additionally, the upregulation of the purine and pyrimidine metabolic routes channels nitrogen resources towards nucleic acid synthesis, and thereby supporting growth. Amino acids are then transported to the seeds, culminating in enhanced seed protein content. This research elucidates the molecular mechanisms underlying the foliar response to urea application, offering significant insights for further investigation. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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15 pages, 4009 KiB  
Article
Metabolomic Profiling and Anti-Helicobacter pylori Activity of Caulerpa lentillifera (Sea Grape) Extract
by Chananchida Thacharoen, Thisirak Inkaewwong, Watthanachai Jumpathong, Pornchai Kaewsapsak, Thiravat Rattanapot and Tippapha Pisithkul
Mar. Drugs 2025, 23(7), 282; https://doi.org/10.3390/md23070282 - 7 Jul 2025
Viewed by 681
Abstract
Helicobacter pylori is a gastric pathogen implicated in peptic ulcer disease and gastric cancer. The increasing prevalence of antibiotic-resistant strains underscores the urgent need for alternative therapeutic strategies. In this study, we investigated the chemical composition and antibacterial activity of an aqueous extract [...] Read more.
Helicobacter pylori is a gastric pathogen implicated in peptic ulcer disease and gastric cancer. The increasing prevalence of antibiotic-resistant strains underscores the urgent need for alternative therapeutic strategies. In this study, we investigated the chemical composition and antibacterial activity of an aqueous extract from Caulerpa lentillifera (sea grape), a farm-cultivated edible green seaweed collected from Krabi Province, Thailand. Ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) revealed that the extract was enriched in bioactive nucleosides and phenolic compounds. In vitro assays demonstrated dose-dependent inhibition of H. pylori growth following exposure to sea grape extract. Furthermore, untargeted intracellular metabolomic profiling of H. pylori cells treated with the extract uncovered significant perturbations in central carbon and nitrogen metabolism, including pathways associated with the tricarboxylic acid (TCA) cycle, one-carbon metabolism, and alanine, aspartate, and glutamate metabolism. Pyrimidine biosynthesis was selectively upregulated, indicating a potential stress-induced shift toward nucleotide salvage and DNA repair. Of particular note, succinate levels were markedly reduced despite accumulation of other TCA intermediates, suggesting disruption of electron transport-linked respiration. These findings suggest that bioactive metabolites from C. lentillifera impair essential metabolic processes in H. pylori, highlighting its potential as a natural source of antimicrobial agents targeting bacterial physiology. Full article
(This article belongs to the Special Issue Marine Omics for Drug Discovery and Development, 2nd Edition)
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21 pages, 3245 KiB  
Article
Interactions of Nedaplatin with Nucleobases and Purine Alkaloids: Their Role in Cancer Therapy
by Kamil Szupryczyński and Beata Szefler
Biomedicines 2025, 13(7), 1551; https://doi.org/10.3390/biomedicines13071551 - 25 Jun 2025
Viewed by 404
Abstract
Background: Nedaplatin is a platinum-based anticancer drug that combines the benefits of Cisplatin and Carboplatin, retaining Cisplatin’s anticancer activity while reducing toxicity similar to Carboplatin. After hydrolysis, Nedaplatin targets purines in DNA and forms cross-links that induce cell death via apoptosis. However, [...] Read more.
Background: Nedaplatin is a platinum-based anticancer drug that combines the benefits of Cisplatin and Carboplatin, retaining Cisplatin’s anticancer activity while reducing toxicity similar to Carboplatin. After hydrolysis, Nedaplatin targets purines in DNA and forms cross-links that induce cell death via apoptosis. However, it is important to consider how the presence of other chemical compounds with structural similarities to Adenine or Guanine, such as aromatic, purine, or pyrimidine compounds containing a nitrogen atom with a free electron pair, might influence its activity at the cellular level. Alkaloids with structures similar to DNA nucleobases are common, and their influence on Nedaplatin’s activity requires investigation. Methods: In this study, the interactions between Nedaplatin (including its hydrolyzed forms, such as [Pt(NH3)2(H2O)2]2+ and [Pt(NH3)2(H2O)(OH)]+) and nucleobases (Adenine and Guanine) and purine alkaloids (Caffeine, Theobromine and Theophylline) were thoroughly investigated using theoretical (density functional theory, DFT) and experimental (UV-Vis spectroscopy) methods. DFT calculations were performed at the B3LYP/6-31G(d,p)/LANL2DZ and MN15/def2-TZVP levels, with structure optimization and harmonic analysis in the gas phase and aqueous solution (modeled using IEF-PCM). UV-Vis spectroscopy was used to verify theoretical findings by examining changes in absorption spectra. Results: Both theoretical and experimental studies confirmed that Nedaplatin forms complexes with both nucleobases and purine alkaloids. Nedaplatin was found to exhibit a higher affinity for nucleobases than for purine alkaloids. Furthermore, this affinity was dependent on the computational method used and on the hydrolyzed form of Nedaplatin. Theoretical calculations showed the formation of stable complexes through bonding with nitrogen atoms in the ligand molecules, which was confirmed by changes in UV-Vis spectra, indicating adduct formation. Conclusions: The results indicate that Nedaplatin readily forms complexes with both nucleobases and purine alkaloids, showing a stronger affinity for nucleobases. This finding highlights the potential importance of Nedaplatin’s interactions with other compounds present in the body, which may influence its effectiveness and mechanism of action in cancer therapy. These studies provide new insights into the molecular mechanisms of Nedaplatin’s action and may contribute to a better understanding of its pharmacological interactions. However, research requires confirmation not only in in vivo studies but also in clinical trials. Full article
(This article belongs to the Special Issue Chemoprevention to Dwindle Tumor Development)
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21 pages, 4310 KiB  
Article
Evaluating Triazole-Substituted Pyrrolopyrimidines as CSF1R Inhibitors
by Srinivasulu Cherukupalli, Jan Eickhoff, Carsten Degenhart, Peter Habenberger, Anke Unger, Bård Helge Hoff and Eirik Sundby
Molecules 2025, 30(12), 2641; https://doi.org/10.3390/molecules30122641 - 18 Jun 2025
Viewed by 678
Abstract
6-Aryl-7H-pyrrolo[2,3-d]pyrimidin-4-amines have promising properties as colony-stimulating factor 1 receptor (CSF1R) inhibitors. Inspired by these antagonists, two series of 1,2,3-triazole analogues (28 compounds) were synthesized and evaluated as CSF1R inhibitors. Enzymatic IC50 profiling showed that 27 of the 28 [...] Read more.
6-Aryl-7H-pyrrolo[2,3-d]pyrimidin-4-amines have promising properties as colony-stimulating factor 1 receptor (CSF1R) inhibitors. Inspired by these antagonists, two series of 1,2,3-triazole analogues (28 compounds) were synthesized and evaluated as CSF1R inhibitors. Enzymatic IC50 profiling showed that 27 of the 28 derivatives had lower IC50 than the reference drug PLX-3397. Three derivatives displayed CSF1R Ba/F3 cellular IC50 well below 1 µM. Profiling of the most promising triazole analogue (compound 27a) toward a panel of kinases reveals a high selectivity for CSF1R with respect to its family kinases, but 27a also inhibits ABL, SRC, and YES kinases. Molecular docking of 27a toward two CSF1R X-ray structures identified two different ligand-inverted binding poses, which triggers interest for further investigations. Full article
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12 pages, 1875 KiB  
Article
Dense Hydrogen-Bonded Assembly of Hydrogen-Rich Cations and Pentazolate Anions: A Series of Highly Insensitive Ionic Salts
by Lianghe Sun, Hongwei Zhu, Shuaijie Jiang, Xiaofeng Yuan, Guoping Lu, Ming Lu and Yuangang Xu
Molecules 2025, 30(12), 2613; https://doi.org/10.3390/molecules30122613 - 16 Jun 2025
Viewed by 514
Abstract
Compounds containing the pentazolate anion (cyclo-N5) represent a distinctive group of energetic materials that have received extensive attention in recent years. Cyclo-N5 was used as a polynitrogen anion for the syntheses of energetic salts through [...] Read more.
Compounds containing the pentazolate anion (cyclo-N5) represent a distinctive group of energetic materials that have received extensive attention in recent years. Cyclo-N5 was used as a polynitrogen anion for the syntheses of energetic salts through metathesis reactions. Propamidinium (1), 5-amino-4-carbamoyl-1H-imidazol-3-ium (2), (1H-1,2,3-triazol-4-yl)methanaminium (3), 5-amino-4H-1,2,4-triazol-1-ium (4), 5-amino-3-methyl-4H-1,2,4-triazol-1-ium (5), and amino(pyrimidin-2-yl)methaniminium (6) pentazolates were obtained with high yields (>80%), and their crystal structures were confirmed through single-crystal X-ray diffraction analyses. Hirshfeld surface analyses and 2D fingerprint plots generated by CrystalExplorer17 demonstrated that these compounds exhibited extensive hydrogen-bonding networks in their crystal packing. Mechanical sensitivity tests showed that all the prepared salts were highly insensitive (IS > 35 J, FS > 360 N), providing valuable insights for the further exploration of broader energetic materials containing cyclo-N5. Full article
(This article belongs to the Special Issue Molecular Design and Synthesis of Novel Energetic Compounds)
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19 pages, 1401 KiB  
Article
Design and Synthesis of Pyridine-Based Pyrrolo[2,3-d]pyrimidine Analogs as CSF1R Inhibitors: Molecular Hybridization and Scaffold Hopping Approach
by Srinivasulu Cherukupalli, Carsten Degenhart, Peter Habenberger, Anke Unger, Jan Eickhoff, Bård Helge Hoff and Eirik Sundby
Pharmaceuticals 2025, 18(6), 814; https://doi.org/10.3390/ph18060814 - 28 May 2025
Viewed by 1567
Abstract
Background/Objectives: Colony stimulating factor 1 receptor kinase (CSF1R) is a well-validated molecular target in drug discovery for various reasons. Based on the structure of an early lead molecule identified in our lab and the marketed drug Pexidartinib (PLX3397), we merged fragments of [...] Read more.
Background/Objectives: Colony stimulating factor 1 receptor kinase (CSF1R) is a well-validated molecular target in drug discovery for various reasons. Based on the structure of an early lead molecule identified in our lab and the marketed drug Pexidartinib (PLX3397), we merged fragments of Pexidartinib with our pyrrolo[2,3-d]pyrimidine nucleus, and the idea was supported by initial molecular docking studies. Thus, several new compounds were synthesized with Pexidartinib fragments on C4, C5, and C6 on the pyrrolopyrimidine scaffold using molecular hybridization. Methods: Nine final products were synthesized using a combination of Buchwald-Hartwig and Suzuki-Miyaura cross-coupling reactions in three to four steps and in good yields. The analogues were subsequently profiled as CSF1R inhibitors in enzymatic and cellular assays, and ADME properties were evaluated for some derivatives. Results: N-Methyl-N-(3-methylbenzyl)-6-(6-((pyridin-3-ylmethyl)amino)pyridin-3-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (12b) emerged as the most potent CSF1R inhibitor, showing low-nanomolar enzymatic activity, cellular efficacy, and favorable ADME properties, highlighting its promise as a lead compound for further development. Conclusions: These findings suggest that combining structural elements from previously reported CSF1R inhibitors such as Pexidartinib could guide the development of improved drug candidates targeting this kinase. Full article
(This article belongs to the Special Issue Design and Synthesis of Small Molecule Kinase Inhibitors)
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21 pages, 10416 KiB  
Article
Combinational Radiotherapies Improve Brain Cancer Treatment at High Dose Rates In Vitro
by Michael Valceski, Elette Engels, Sarah Vogel, Jason Paino, Dylan Potter, Carolyn Hollis, Abass Khochaiche, Micah Barnes, Alice O’Keefe, Matthew Cameron, Kiarn Roughley, Anatoly Rosenfeld, Michael Lerch, Stéphanie Corde and Moeava Tehei
Cancers 2025, 17(10), 1713; https://doi.org/10.3390/cancers17101713 - 20 May 2025
Viewed by 3215
Abstract
Background/objectives: Brain cancer remains difficult to treat, with survival statistics stagnant for decades. The resistance of glioblastoma brain tumours can greatly challenge the effectiveness of conventional cancer radiotherapy. However, high dose rate radiotherapy has unique effects that allow for normal tissue sparing whilst [...] Read more.
Background/objectives: Brain cancer remains difficult to treat, with survival statistics stagnant for decades. The resistance of glioblastoma brain tumours can greatly challenge the effectiveness of conventional cancer radiotherapy. However, high dose rate radiotherapy has unique effects that allow for normal tissue sparing whilst maintaining tumour control. The addition of targeted radiosensitisers, such as the chemotherapeutic drug methotrexate (MTX) or the high-Z halogenated pyrimidine drug iododeoxyuridine (IUdR), can improve radiotherapy outcomes. Combining these radiosensitiser agents with ultra-high dose rate (UHDR) synchrotron X-rays can bear synergistic effects to enhance the efficacy of these multi-modal UHDR therapies, providing a means to overcome the radioresistance of brain cancer. Methods: Here, we use controlled in vitro assays following treatment, including a clonogenic assay to determine long-term cell survival and γH2AX immunofluorescent confocal microscopy to quantify double-strand DNA breaks (DSBs). Results: We find significant enhancement for highly synergistic combinations of IUdR+MTX with synchrotron X-rays. Cell survival results demonstrate 5.4 times increased 9L gliosarcoma cell killing when these agents are combined with UHDR synchrotron X-rays compared with conventional X-rays alone at the same 5 Gy dose. The underlying mechanisms are unveiled using γH2AX imaging and reveal significant increases in DSBs and dying cells following exposure to UHDR radiation. Conclusions: Our results demonstrate that highly synergistic combination treatments using UHDR synchrotron radiation can yield significantly improved brain cancer killing compared with conventional radiotherapy. We anticipate that these additive, multi-modal combination therapies will provide options for more targeted and effective use of radiotherapies for the future treatment of brain cancer. Full article
(This article belongs to the Section Cancer Therapy)
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20 pages, 6531 KiB  
Article
Bacillus subtilis-Derived Postbiotics as a Multifunctional Bio-Catalyst for Enhancing Lactic Acid Bacteria Viability and Yogurt Quality
by Jing Wu, Zhilin Wang, Jingyi Hu, Jing Liu, Xueying Han, Hongping Chen, Siming Zhu and Junjin Deng
Foods 2025, 14(10), 1806; https://doi.org/10.3390/foods14101806 - 19 May 2025
Cited by 1 | Viewed by 803
Abstract
This study demonstrates that Bacillus subtilis GDAAS-A32-derived postbiotics (BSP) enhance yogurt production by optimizing lactic acid bacteria (LAB) viability and functionality. BSP enhanced the growth kinetics and biomass accumulation of Streptococcus thermophilus and Lactobacillus bulgaricus in both an anaerobic and aerobic pure system. [...] Read more.
This study demonstrates that Bacillus subtilis GDAAS-A32-derived postbiotics (BSP) enhance yogurt production by optimizing lactic acid bacteria (LAB) viability and functionality. BSP enhanced the growth kinetics and biomass accumulation of Streptococcus thermophilus and Lactobacillus bulgaricus in both an anaerobic and aerobic pure system. The addition of BSP significantly increased the viable cell counts of S. thermophilus and L. bulgaricus, milk-clotting activity, sensory properties, and extracellular polysaccharide content and improved the rheological properties. Moreover, BSP elevated viable counts of S. thermophilus and L. bulgaricus to 6.18 × 108 CFU/g and 1.03 × 108 CFU/g, respectively, by day 7—representing 11.3-fold and 9.3-fold increases versus controls at 20% supplementation. Metabolomic signatures confirmed peptidoglycan reinforcement and flavor enhancement. Mechanistically, BSP supplementation might reduce urate and H2O2 toxicity through NH3-mediated proton neutralization and oxygen scavenging, while establishing a pyrimidine salvage network and redirecting one-carbon metabolism, resulting in enhanced stress tolerance and significant improvements in bacterial viability. Full article
(This article belongs to the Section Dairy)
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19 pages, 6195 KiB  
Article
Identification of Novel HPK1 Hit Inhibitors: From In Silico Design to In Vitro Validation
by Israa H. Isawi, Rayan M. Obeidat, Soraya Alnabulsi and Rufaida Al Zoubi
Int. J. Mol. Sci. 2025, 26(9), 4366; https://doi.org/10.3390/ijms26094366 - 4 May 2025
Viewed by 839
Abstract
Hematopoietic progenitor kinase 1 (HPK1), a negative regulator of T-cells, B-cells, and dendritic cells, has gained attention in antitumor immunotherapy research over the past decade. No HPK1 inhibitor has yet reached clinical approval, largely due to selectivity and drug-like limitations. Leveraging the available [...] Read more.
Hematopoietic progenitor kinase 1 (HPK1), a negative regulator of T-cells, B-cells, and dendritic cells, has gained attention in antitumor immunotherapy research over the past decade. No HPK1 inhibitor has yet reached clinical approval, largely due to selectivity and drug-like limitations. Leveraging the available structural insights into HPK1, we conducted a rational hit identification using a structure-based virtual screening of over 600,000 drug-like molecules from ASINEX and OTAVA databases. A series of molecular docking studies, in vitro kinase assays, and molecular dynamics simulations were conducted to identify viable HPK1 inhibitor hits. This approach resulted in two promising novel hit scaffolds, 4H-Pyrido[1,2-a] thieno[2,3-d] pyrimidin-4-one (ISR-05) and quinolin-2(1H)-one (ISR-03), neither of which has previously been reported as an HPK1 inhibitor. ISR-05 and ISR-03 exhibited IC50 values of 24.2 ± 5.07 and 43.9 ± 0.134 µM, respectively, in kinase inhibition assays. These hits constitute tractable starting points for future hit-to-lead optimization aimed at developing more effective HPK1 inhibitors for cancer therapy. Full article
(This article belongs to the Section Molecular Informatics)
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31 pages, 8352 KiB  
Article
Novel Trimethoprim-Based Metal Complexes and Nanoparticle Functionalization: Synthesis, Structural Analysis, and Anticancer Properties
by Abbas M. Abbas, Hossam H. Nasrallah, A. Aboelmagd, W. Christopher Boyd, Haitham Kalil and Adel S. Orabi
Inorganics 2025, 13(5), 144; https://doi.org/10.3390/inorganics13050144 - 1 May 2025
Viewed by 888
Abstract
In this study, we synthesized a novel trimethoprim derivative, 4-(((2-amino-5-(3,4,5-trimethoxybenzyl) pyrimidine-4-yl)imino)methyl)benzene-1,3-diol (HD), by the reaction of trimethoprim with 2,4-dihydroxybenzaldehyde. We then prepared metal complexes of this derivative with Cu(II), Co(II), Ni(II), Ag(I), and Zn(II) and functionalized them with ZnO and Au nanoparticles. Their [...] Read more.
In this study, we synthesized a novel trimethoprim derivative, 4-(((2-amino-5-(3,4,5-trimethoxybenzyl) pyrimidine-4-yl)imino)methyl)benzene-1,3-diol (HD), by the reaction of trimethoprim with 2,4-dihydroxybenzaldehyde. We then prepared metal complexes of this derivative with Cu(II), Co(II), Ni(II), Ag(I), and Zn(II) and functionalized them with ZnO and Au nanoparticles. Their structures were confirmed through 1H NMR, mass spectrometry, FTIR, conductivity, thermal analysis, magnetic susceptibility, X-ray diffraction, UV-Vis spectroscopy, and TEM, revealing octahedral geometries for all complexes. Surface features were investigated using density functional theory (DFT) analysis. Pharmacokinetic parameters and target enzymes for HD and its complexes were computed using the SwissADME web tool, with the BOILED-Egg model indicating that HD and its Cu complex should be passively permeable via the blood-brain barrier and highly absorbed by the gastrointestinal tract (GIT), unlike the Ni, Co, Ag, and Zn complexes, which are predicted to show low GIT absorption. Molecular docking studies with the Caspase-3 enzyme (PDB code: 3GJQ) using the AutoDock 4.2 software demonstrated binding energies of −7.66, −8.36, −9.05, −8.62, −6.90, and −7.81 kcal/mol for HD and the Cu, Co, Ni, Ag, and Zn complexes, respectively, compared to −6.54 and −4.63 kcal/mol for TMP and 5-FU (5-fluorouracil), indicating a potential superior anticancer potential of the novel compounds. The anticancer activities of these complexes were evaluated using the MTT assay. The IC50 values for 5-FU, TMP, HD, Cu-HD, HD@ZnONPs, Cu-HD@ZnONPs, HD@AuNPs, and Cu-HD@AuNPs were found to be 32.53, 80.76, 114.7, 61.66, 77, 53.13, 55.06, and 50.81 µg/mL, respectively. Notably, all derivatives exhibited higher activity against the HepG-2 cancer cell line than TMP, except for HD, which showed similar effectiveness to TMP. Real-time PCR analysis revealed that the Au-HD@AuNPs and Cu-HD@AuNPs significantly increased caspase-3 inhibition by 4.35- and 4.5-fold and P53 expression by 3.05- and 3.41-fold, respectively, indicating enhanced pro-apoptotic gene expression and apoptosis induction in HepG2 cells. Our findings demonstrate that these novel derivatives possess significant anticancer properties, with some complexes showing superior activity compared to standard drugs such as 5-Fluorouracil (5-FU) and Trimethoprim (TMP). This study highlights the potential of these nanocomposites as promising candidates for cancer therapy. Full article
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