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84 results for “Pyrimidines”
Supplementary Information for "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus"
<p>This is the external Supplementary Information for our publication "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from <em>Thermus thermophilus</em>".</p> <p>The .pdf file contains the Supplementary Information: author contributions, experimental procedures and supplementary items.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) and the calculations.</p> <p>The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publications (10.3390/mps2030060, 10.5281/zenodo.3333469, 10.1002/cbic.202000204, 10.5281/zenodo.3723806 ). Further applications of this method can be found in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858).</p>
Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis
<p>This study elucidates the essential role of pyrimidines in supporting mitochondrial pyruvate oxidation and the tricarboxylic acid (TCA) cycle. Quantitative assessment of metabolite changes in response to alterations in cellular pyrimidine levels was conducted using liquid chromatography-mass spectrometry. Concurrently, western blot analysis was employed to characterize the expression of metabolic enzymes potentially involved in this regulatory process. To enhance precision, metabolic activity measurements were conducted under both untreated and pyrimidine-depleted conditions using radioactivity-based assays, isotope tracers, and Seahorse analyzers. The comprehensive dataset includes experimental quantifications of metabolite abundance, accurate assessments of metabolic activity, and protein levels of metabolic and signaling enzymes.</p>
Source data for the publication "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time", Nature Communications, 2021
<p>The archives contain the raw data used to generate the transient absorption spectra for uridine (Figure 1) and 5-methyluridine (Figure 2) presented in the main paper, as well as the trajectory plots and auxiliary spectra presented in the Supplementary Information of the paper "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time" authored by R. Borrego-Varillas et al. published in Nature Communications, 2021. Specifically:</p> <p><strong>URD</strong>: folder with raw data from the uridine trajectories (56 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory</p> <p><strong>5mURD</strong>: folder with raw data from the 5-methyluridine trajectories (57 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory</p> <p>The raw data of each trajectory is inside a folder named <em>geom_XXX</em> where <em>XXX</em> stands for a 3-digit label of the trajectory. The trajectories have been selected out of a pool of 500 trajectories according to the S0-S1 vertical gap so that only trajectories whose energy gap falls under the envelope of the pulse are selected</p> <p><strong>URD</strong>: 003 005 006 011 015 023 039 040 054 056 060 083 098 104 112 114 116 121 122 147 152 158 161 171 173 175 177 186 189 200 204 211 219 223 225 232 234 235 236 246 251 252 257 259 265 268 271 272 279 286 287 289 305 313 318 336</p> <p><strong>5mURD</strong>: 010 044 045 048 052 057 065 074 085 094 097 099 100 105 110 112 113 121 131 137 138 140 144 145 159 164 170 179 182 183 184 186 189 199 203 205 209 214 219 220 221 239 243 250 251 273 284 290 295 301 302 320 325 327 328 333 334</p> <p>In each geom_XXX folder there are following files:</p> <p><strong>S1-S<em>Y</em>.dat</strong>: ASCII files () in which the individual columns correspond to </p> <p>col1: time [fs] </p> <p>col2: transition energy of state S<em>Y</em> with respect to S1 [cm-1] where S0 is the ground state</p> <p>col3-5: X, Y and Z components of the transition dipole moment between S1 and S<em>Y</em> [a.u.]</p> <p>col6: magnitude of the transition dipole moment between S1 and S<em>Y</em> [a.u.] </p> <p>col7: angle between transition dipole moment at time t and t=0 [deg]</p> <p>Note that in URD S1-S0.dat contains in most cases about 500 data points (0-500 fs), in 5mURD S1-S0.dat contains 1000 data points (0-1000 fs) except for a few cases in which the trajectories were interrupted earlier. This data has been used to simulate the stimulated emission before the hopping event and the hot ground state photoinduced absorption after hopping. S1-S<em>Y</em>.dat () contain only data points until the hopping event which have been used to simulate the excited state photoinduced absorption.</p> <p>The spectra reported in the main article (Figs 1 & 2) as well as in the SI can be reproduced following eq. 13-18 in the Supplementary Information.</p> <p> </p> <p><strong>HighMediumLayer_traj.xyz.zip</strong>: archived Cartesian coordinates of the High Layer (nucleobase) and Medium Layer (sugar and waters within 5 Å distance from nucleobase) along the dynamics</p> <p>Note that due to the different number of waters in each trajectory the size of the Medium layer (and thus the size of the system) may vary from trajectory to trajectory.</p> <p>Note that due to the different duration of each trajectory the number of geometries may vary from trajectory to trajectory.</p> <p><strong>LowLayer.xyz:</strong> Cartesian coordinates of the Low Layer (waters > 5 Å from the nucleobase); the coordinates of these waters are kept fixed along the trajectory.</p> <p>The coordinates of High, Medium and Low layers can be used to reproduce the QMMM calculations (energies, gradients and transition dipole moments along each trajectory) with the official COBRAMM release (<a href="https://gitlab.com/cobrammgroup/cobramm.git">https://gitlab.com/cobrammgroup/cobramm.git</a>) following the parameters provided in Supplementary Note 2 of the Supplementary Information.</p>
potassium (2-pyrimidin-2-yl-1H-benzimidazole)dimethylnickel, K(bimpm)Ni(CH3)2
<p>Data Set for compound 1</p>
Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis
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Synthesis, Herbicidal Activity, Crop Safety and Soil Degradation of Pyrimidine- and Triazine-Substituted Chlorsulfuron Derivatives Supplementary Information
<p>The content include SI1-Melting points, 1H-NMR, 13C-NMR and HRMS of W103-W111, SI2-Crystal data of compound W110(CCDC number 2142702), SI3-Biological assay and crop safety, SI4-Soil degradation assay, SI5-Report of soil analysis in Chinese, and SI6-Report of soil analysis in English.</p>
Deoxynucleosides Pyrimidines as Treatment for Mitochondrial Depletion Syndrome
ClinicalTrials.gov study NCT04802707. IPD Sharing: YES. Countries: 1. Publications: 67.
Data for: Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics
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Fig. 5 in Floro-pyrazolo[3,4-d]pyrimidine derivative as a novel plant activator induces two-pathway immune system
Fig. 5. The synthetic route of 1-methyl-4-substituted phenylamino pyrazolo [3,4-d] pyrimidine derivatives (P1).
Fig. 7 in Floro-pyrazolo[3,4-d]pyrimidine derivative as a novel plant activator induces two-pathway immune system
Fig. 7. The synthetic route of N-(1-methyl-1H-pyrazolo [3,4-d]pyrimidin-4-yl) substituted carboxamide derivatives (P3).
Fig. 6 in Floro-pyrazolo[3,4-d]pyrimidine derivative as a novel plant activator induces two-pathway immune system
Fig. 6. The synthetic route of 1-methyl-4-substituted ether pyrazolo [3,4-d] pyrimidine derivatives (P2).
Fig. 4 in Floro-pyrazolo[3,4-d]pyrimidine derivative as a novel plant activator induces two-pathway immune system
Fig. 4. Gene expression in Arabidopsis thaliana after treatment of chemicals. Bars (gray, PR1; black, PDF1.2) denote the mean ± STD of three independent biological replicates. (***P <0.01; **P <0.05; one-tailed t-test).
An Open-Label Study of Continuation Treatment With Combination Pyrimidine Nucleosides in Patients With TK2 Deficiency
ClinicalTrials.gov study NCT03845712. IPD Sharing: YES. Countries: 3. Publications: 1.
Targeting de Novo Pyrimidine Biosynthesis by Leflunomide for the Treatment of COVID-19 Virus Disease
ClinicalTrials.gov study NCT05007678. IPD Sharing: YES. Countries: 1. Publications: 1.
A Natural History Study Seeks to Understand the Clinical, Genomic, Pharmacological, Laboratory, and Dietary Determinates of Pyrimidine and Purine Metabolism Disorders
ClinicalTrials.gov study NCT06092346. IPD Sharing: UNDECIDED. Countries: 1. Publications: 7.
Figure 8 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 8 Structures of compounds 7 (octanoyl derivative), 9 (myristoyl derivative), and 14 (dichloroacetyl derivative).
Scheme 1 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Scheme 1 Reagents and conditions: (a) dry Py, (C6H5)3COCl, –5 °C, 6 h, (70%; Rf = 0.52); (b) dry Py, various acyl halides (3–14), 0 °C to rt, DMAP, 6 h.
Figure 5 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 5 Percentage zone of mycelial growth inhibition for compounds 3 and 11 against A. niger (A and B, respectively). DMSO represents the negative control, whereas nystatin is the positive control.
Figure 2 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 2 Percentage of inhibition observed for A) B. subtilis by compounds 7, 9, and 8; B) E. coli by compounds 2, 4, and 9; C) S. abony by compounds 7, 9, and 14; and D) S. aureus by compounds 7, 9, and 14. DMSO was the negative control, whereas azithromycin represented the positive control.
Figure 7 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 7 Percentage growth inhibition observed for various concentrations of compound 9. Right figure 96-well flat-bottom experiment.
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