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ACS Omega Apr 2024Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs)...
Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations.
Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for design/optimization of new NBTIs. Utilizing NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for ( = 0.791) and ( = 0.806). Both models accurately predicted the ICs of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against and DNA gyrase. We are confident that this integrated modeling approach could be valuable in the design and optimization of efficient NBTIs for combating resistant bacterial pathogens.
PubMed: 38680300
DOI: 10.1021/acsomega.4c00036 -
Immunity, Inflammation and Disease Apr 2024Ulcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa, with a gradually increasing incidence. Therefore, it is necessary to actively seek...
BACKGROUND
Ulcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa, with a gradually increasing incidence. Therefore, it is necessary to actively seek targets for the treatment of UC.
METHODS
Common differentially expressed genes (DEGs) were screened from two microarray data sets related to UC. Protein-protein interaction network was constructed to find the hub genes. The UC mouse model and cell model were induced by dextran sulfate sodium (DSS). The pathological changes of colon tissue were observed by hematoxylin-eosin staining. Immunohistochemistry and immunofluorescence were performed to detect the expressions of Ki67 and Claudin-1. The performance of mice was observed by disease activity index (DAI). The effect of TOP2A on proliferation, inflammation, oxidative stress, and interleukin-17 (IL-17) signaling pathway in UC model was measured by cell counting kit-8, enzyme-linked immunosorbent assay, and western blot.
RESULTS
Through bioinformatics analysis, 295 common DEGs were screened, and the hub gene TOP2A was selected. In UC model, there was obvious inflammatory cell infiltration in the colon and less goblet cells, while si-TOP2A lessened it. More Ki67 positive cells and less Claudin-1 positive cells were observed in UC model mice. Furthermore, knockdown of TOP2A increased the body weight and colon length of UC mice, while the DAI was decreased. Through in vivo and in vitro experiments, knockdown of TOP2A also inhibited inflammation and IL-17 signaling pathway, and promoted proliferation in DSS-induced NCM460 cells.
CONCLUSION
Knockdown of TOP2A alleviated the progression of UC by suppressing inflammation and inhibited IL-17 signaling pathway.
Topics: Animals; Humans; Male; Mice; Colitis, Ulcerative; Dextran Sulfate; Disease Models, Animal; Disease Progression; DNA Topoisomerases, Type II; Gene Knockdown Techniques; Interleukin-17; Poly-ADP-Ribose Binding Proteins; Protein Interaction Maps; Signal Transduction
PubMed: 38661103
DOI: 10.1002/iid3.1207 -
Angewandte Chemie (International Ed. in... Jul 2024A planar conjugated ligand functionalized with bithiophene and its Ru(II), Os(II), and Ir(III) complexes have been constructed as single-molecule platform for...
A planar conjugated ligand functionalized with bithiophene and its Ru(II), Os(II), and Ir(III) complexes have been constructed as single-molecule platform for synergistic photodynamic, photothermal, and chemotherapy. The complexes have significant two-photon absorption at 808 nm and remarkable singlet oxygen and superoxide anion production in aqueous solution and cells when exposed to 808 nm infrared irradiation. The most potent Ru(II) complex Ru7 enters tumor cells via the rare macropinocytosis, locates in both nuclei and mitochondria, and regulates DNA-related chemotherapeutic mechanisms intranuclearly including DNA topoisomerase and RNA polymerase inhibition and their synergistic effects with photoactivated apoptosis, ferroptosis and DNA cleavage. Ru7 exhibits high efficacy in vivo for malignant melanoma and cisplatin-resistant non-small cell lung cancer tumors, with a 100 % survival rate of mice, low toxicity to normal cells and low residual rate. Such an infrared two-photon activatable metal complex may contribute to a new generation of single-molecule-based integrated diagnosis and treatment platform to address drug resistance in clinical practice and phototherapy for large, deeply located solid tumors.
Topics: Coordination Complexes; Animals; Humans; Antineoplastic Agents; Infrared Rays; Photons; Thiophenes; Mice; Photochemotherapy; Photosensitizing Agents; Ruthenium; Cell Line, Tumor; Drug Screening Assays, Antitumor; Photothermal Therapy; Iridium; Molecular Structure; Apoptosis
PubMed: 38656658
DOI: 10.1002/anie.202402028 -
Scientific Reports Apr 2024Oral malignancies continue to have severe morbidity with less than 50% long-term survival despite the advancement in the available therapies. There is a persisting...
Oral malignancies continue to have severe morbidity with less than 50% long-term survival despite the advancement in the available therapies. There is a persisting demand for new approaches to establish more efficient strategies for their treatment. In this regard, the human topoisomerase II (topoII) enzyme is a validated chemotherapeutics target, as topoII regulates vital cellular processes such as DNA replication, transcription, recombination, and chromosome segregation in cells. TopoII inhibitors are currently used to treat some neoplasms such as breast and small cells lung carcinomas. Additionally, topoII inhibitors are under investigation for the treatment of other cancer types, including oral cancer. Here, we report the therapeutic effect of a tetrahydroquinazoline derivative (named ARN21934) that preferentially inhibits the alpha isoform of human topoII. The treatment efficacy of ARN21934 has been evaluated in 2D cell cultures, 3D in vitro systems, and in chick chorioallantoic membrane cancer models. Overall, this work paves the way for further preclinical developments of ARN21934 and possibly other topoII alpha inhibitors of this promising chemical class as a new chemotherapeutic approach for the treatment of oral neoplasms.
Topics: Humans; DNA Topoisomerases, Type II; Topoisomerase II Inhibitors; Squamous Cell Carcinoma of Head and Neck; Cell Line, Tumor; Animals; Quinazolines; Cell Proliferation; Head and Neck Neoplasms; Antineoplastic Agents; Chick Embryo
PubMed: 38644364
DOI: 10.1038/s41598-024-59592-5 -
Journal of Molecular Biology May 2024DNA mismatch repair endonuclease MutL is a member of GHKL ATPase superfamily. Mutations of MutL homologs are causative of a hereditary cancer, Lynch syndrome. We...
DNA mismatch repair endonuclease MutL is a member of GHKL ATPase superfamily. Mutations of MutL homologs are causative of a hereditary cancer, Lynch syndrome. We characterized MutL homologs from human and a hyperthermophile, Aquifex aeolicus, (aqMutL) to reveal the catalytic mechanism for the ATPase activity. Although involvement of a basic residue had not been conceived in the catalytic mechanism, analysis of the pH dependence of the aqMutL ATPase activity revealed that the reaction is catalyzed by a residue with an alkaline pK. Analyses of mutant aqMutLs showed that Lys79 is the catalytic residue, and the corresponding residues were confirmed to be critical for activities of human MutL homologs, on the basis of which a catalytic mechanism for MutL ATPase is proposed. These and other results described here would contribute to evaluating the pathogenicity of Lynch syndrome-associated missense mutations. Furthermore, it was confirmed that the catalytic lysine residue is conserved among DNA gyrases and microrchidia ATPases, other members of GHKL ATPases, indicating that the catalytic mechanism proposed here is applicable to these members of the superfamily.
Topics: Humans; Adenosine Triphosphatases; Amino Acid Sequence; Catalysis; Catalytic Domain; Conserved Sequence; Hydrogen-Ion Concentration; Lysine; MutL Proteins; Transcription Factors; DNA Gyrase; DNA-Binding Proteins
PubMed: 38641238
DOI: 10.1016/j.jmb.2024.168575 -
Molecular Cell Apr 2024The DNA topological challenges generated by cellular manipulation of extremely long DNA fibers remain poorly understood. In this issue of Molecular Cell, Hildebrand...
The DNA topological challenges generated by cellular manipulation of extremely long DNA fibers remain poorly understood. In this issue of Molecular Cell, Hildebrand et al. describe how mitotic chromosomes are self entangled and that disentanglement requires TOP2 activity in late mitosis.
Topics: DNA Topoisomerases, Type II; Chromosomes; DNA; Mitosis
PubMed: 38640891
DOI: 10.1016/j.molcel.2024.03.025 -
Chemistry & Biodiversity Jun 2024In this study, several imidazole derivatives in one pot multicomponent reaction from various aldehydes 1(a-z), 9,10-phenanthrenequinone, or benzyl (2), and ammonium...
In this study, several imidazole derivatives in one pot multicomponent reaction from various aldehydes 1(a-z), 9,10-phenanthrenequinone, or benzyl (2), and ammonium acetate (3) were synthesized in the presence of acetic acid (AcOH) under reflux conditions at 120 °C. Also, the photochromic properties of synthesized compounds were investigated in AcOH as a solvent under laboratory conditions at a temperature of 120 °C. Moreover, the antibacterial activity of the synthesized compounds was investigated. The structure of the products was confirmed using FT-IR, UV-Vis, H-NMR, and CNMR spectroscopy. The antimicrobial activity of these compounds against gram-positive bacteria including Bacillus subtilis (B. subtilis) and gram-negative bacteria including Escherichia coli (E.coli) bacteria was evaluated by the Well diffusion (WD) method, and the compounds 4 o showed significant results for both antibacterial activity. To gain insight into how these compounds interact with two types of targets, i. e., human topoisomerase II alpha (5GWK) and acetylcholinesterase (7AIX), binding calculations have been used that provide significant results for both targets and show that most ligands can effectively bind to cleft nucleotides. Interfere in the first one or be well placed in them. Hydrophobic pocket in the dimension, which can ultimately lead to high scores achieved.
Topics: Anti-Bacterial Agents; Imidazoles; Microbial Sensitivity Tests; Molecular Docking Simulation; Humans; Structure-Activity Relationship; Bacillus subtilis; DNA Topoisomerases, Type II; Escherichia coli; Acetylcholinesterase; Molecular Structure; Phenanthrenes; Dose-Response Relationship, Drug
PubMed: 38635369
DOI: 10.1002/cbdv.202400325 -
The American Journal of Pathology Jul 2024Because the mechanotransduction by stromal stiffness stimulates the rupture and repair of the nuclear envelope in pancreatic progenitor cells, accumulated genomic...
Because the mechanotransduction by stromal stiffness stimulates the rupture and repair of the nuclear envelope in pancreatic progenitor cells, accumulated genomic aberrations are under selection in the tumor microenvironment. Analysis of cell growth, micronuclei, and phosphorylated Ser-139 residue of the histone variant H2AX (γH2AX) foci linked to mechanotransduction pressure in vivo during serial orthotopic passages of mouse Kras;Trp53;Pdx1-Cre (KPC) cancer cells in the tumor and in migrating through the size-restricted 3-μm micropores. To search for pancreatic cancer cell-of-origin, analysis of single-cell data sets revealed that the extracellular matrix shaped an alternate route of acinar-ductal transdifferentiation of acinar cells into topoisomerase II α (TOP2A)-overexpressing cancer cells and derived subclusters with copy number amplifications in MYC-PTK2 (protein tyrosine kinase 2) locus and PIK3CA. High-PTK2 expression is associated with 171 differentially methylated CpG loci, 319 differentially expressed genes, and poor overall survival in The Cancer Genome Atlas-Pancreatic Adenocarcinoma cohort. Abolished RGD-integrin signaling by disintegrin KG blocked the PTK2 phosphorylation, increased cancer apoptosis, decreased vav guanine nucleotide exchange factor 1 (VAV1) expression, and prolonged overall survival in the KPC mice. Reduction of α-smooth muscle actin deposition in the CD248 knockout KPC mice remodeled the tissue stroma and down-regulated TOP2A expression in the epithelium. In summary, stromal stiffness induced the onset of cancer cells-of-origin by ectopic TOP2A expression, and the genomic amplification of MYC-PTK2 locus via alternative transdifferentiation of pancreatic progenitor cells is the vulnerability useful for disintegrin KG treatment.
Topics: Animals; Pancreatic Neoplasms; Mice; Disease Progression; Chromosomal Instability; Humans; Carcinoma in Situ; Stromal Cells; Tumor Microenvironment; Mechanotransduction, Cellular; Focal Adhesion Kinase 1
PubMed: 38631549
DOI: 10.1016/j.ajpath.2024.02.023 -
Helicobacter 2024The current standard treatment for Helicobacter pylori infection, which involves a combination of two broad-spectrum antibiotics, faces significant challenges due to its...
BACKGROUND
The current standard treatment for Helicobacter pylori infection, which involves a combination of two broad-spectrum antibiotics, faces significant challenges due to its detrimental impact on the gut microbiota and the emergence of drug-resistant strains. This underscores the urgent requirement for the development of novel anti-H. pylori drugs. Zoliflodacin, a novel bacterial gyrase inhibitor, is currently undergoing global phase III clinical trials for treating uncomplicated Neisseria gonorrhoeae. However, there is no available data regarding its activity against H. pylori.
MATERIALS AND METHODS
We evaluated the in vitro activity of zoliflodacin against H. pylori clinical isolates (n = 123) with diverse multidrug resistance. We performed DNA gyrase supercoiling and microscale thermophoresis assays to identify the target of zoliflodacin in H. pylori. We analyzed 2262 H. pylori whole genome sequences to identify Asp424Asn and Lys445Asn mutations in DNA gyrase subunit B (GyrB) that are associated with zoliflodacin resistance.
RESULTS
Zoliflodacin exhibits potent activity against all tested isolates, with minimal inhibitory concentration (MIC) values ranging from 0.008 to 1 μg/mL (MIC: 0.125 μg/mL; MIC: 0.25 μg/mL). Importantly, there was no evidence of cross-resistance to any of the four first-line antibiotics commonly used against H. pylori. We identified GyrB as the primary target of zoliflodacin, with Asp424Asn or Lys445Asn substitutions conferring resistance. Screening of 2262 available H. pylori genomes for the two mutations revealed only one clinical isolate carrying Asp424Asn substitution.
CONCLUSION
These findings support the potential of zoliflodacin as a promising candidate for H. pylori treatment, warranting further development and evaluation.
Topics: Humans; Anti-Bacterial Agents; Barbiturates; DNA Gyrase; Drug Resistance, Bacterial; Helicobacter Infections; Helicobacter pylori; Isoxazoles; Microbial Sensitivity Tests; Morpholines; Oxazolidinones; Spiro Compounds; Clinical Trials, Phase III as Topic
PubMed: 38627919
DOI: 10.1111/hel.13075 -
Scientific Reports Apr 2024
PubMed: 38627539
DOI: 10.1038/s41598-024-59332-9