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Nature Communications May 2017Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable...
Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides. We present a divergent synthesis of pyrimidine and 8-oxo-purine nucleotides starting from a common prebiotic precursor that yields the β-ribo-stereochemistry found in the sugar phosphate backbone of biological nucleic acids. The generational relationship between pyrimidine and 8-oxo-purine nucleotides suggests that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids prior to the emergence of the canonical nucleotides of biology.
Topics: Furans; Oxazoles; Pentoses; Phosphorylation; Prebiotics; Purine Nucleotides; Purines; Pyrimidines; Ribonucleotides; Stereoisomerism; Sugars; Thiones
PubMed: 28524845
DOI: 10.1038/ncomms15270 -
Journal of the American Chemical Society Jul 2014Thymidylate is a critical DNA nucleotide that has to be synthesized in cells de novo by all organisms. Flavin-dependent thymidylate synthase (FDTS) catalyzes the final...
Thymidylate is a critical DNA nucleotide that has to be synthesized in cells de novo by all organisms. Flavin-dependent thymidylate synthase (FDTS) catalyzes the final step in this de novo production of thymidylate in many human pathogens, but it is absent from humans. The FDTS reaction proceeds via a chemical route that is different from its human enzyme analogue, making FDTS a potential antimicrobial target. The chemical mechanism of FDTS is still not understood, and the two most recently proposed mechanisms involve reaction intermediates that are unusual in pyrimidine biosynthesis and biology in general. These mechanisms differ in the relative timing of the reaction of the flavin with the substrate. The consequence of this difference is significant: the intermediates are cationic in one case and neutral in the other, an important consideration in the construction of mechanism-based enzyme inhibitors. Here we test these mechanisms via chemical trapping of reaction intermediates, stopped-flow, and substrate hydrogen isotope exchange techniques. Our findings suggest that an initial activation of the pyrimidine substrate by reduced flavin is required for catalysis, and a revised mechanism is proposed on the basis of previous and new data. These findings and the newly proposed mechanism add an important piece to the puzzle of the mechanism of FDTS and suggest a new class of intermediates that, in the future, may serve as targets for mechanism-based design of FDTS-specific inhibitors.
Topics: Enzyme Activation; Flavins; Oxidation-Reduction; Pyrimidines; Substrate Specificity; Thermotoga maritima; Thymidylate Synthase
PubMed: 25025487
DOI: 10.1021/ja506108b -
Journal of Dairy Science Nov 2022The purpose of this study was to evaluate the effect of 6 different feeding systems (based on corn silage as the main ingredient) on the chemical composition of milk and...
The purpose of this study was to evaluate the effect of 6 different feeding systems (based on corn silage as the main ingredient) on the chemical composition of milk and to highlight the potential of untargeted metabolomics to find discriminant marker compounds of different nutritional strategies. Interestingly, the multivariate statistical analysis discriminated milk samples mainly according to the high-moisture ear corn (HMC) included in the diet formulation. Overall, the most discriminant compounds, identified as a function of the HMC, belonged to AA (10 compounds), peptides (71 compounds), pyrimidines (38 compounds), purines (15 compounds), and pyridines (14 compounds). The discriminant milk metabolites were found to significantly explain the metabolic pathways of pyrimidines and vitamin B. Interestingly, pathway analyses revealed that the inclusion of HMC in the diet formulation strongly affected the pyrimidine metabolism in milk, determining a significant up-accumulation of pyrimidine degradation products, such as 3-ureidopropionic acid, 3-ureidoisobutyric acid, and 3-aminoisobutyric acid. Also, some pyrimidine intermediates (such as l-aspartic acid, N-carbamoyl-l-aspartic acid, and orotic acid) were found to possess a high discrimination degree. Additionally, our findings suggested that the inclusion of alfalfa silage in the diet formulation was potentially correlated with the vitamin B metabolism in milk, being 4-pyridoxic acid (a pyridoxal phosphate degradation product) the most significant and up-accumulated compound. Taken together, the accumulation trends of different marker compounds revealed that both pyrimidine intermediates and degradation products are potential marker compounds of HMC-based diets, likely involving a complex metabolism of microbial nitrogen based on total splanchnic fluxes from the rumen to mammary gland in dairy cows. Also, our findings highlight the potential of untargeted metabolomics in both foodomics and foodomics-based studies involving dairy products.
Topics: Cattle; Female; Animals; Silage; Milk; Zea mays; Orotic Acid; Aspartic Acid; Pyridoxal Phosphate; Pyridoxic Acid; Lactation; Fermentation; Rumen; Pyrimidines; Medicago sativa; Diet; Nitrogen; Metabolome; Purines; Vitamins
PubMed: 36175222
DOI: 10.3168/jds.2022-21903 -
Leukemia Apr 2021Mechanisms-of-resistance to decitabine and 5-azacytidine, mainstay treatments for myeloid malignancies, require investigation and countermeasures. Both are nucleoside...
Mechanisms-of-resistance to decitabine and 5-azacytidine, mainstay treatments for myeloid malignancies, require investigation and countermeasures. Both are nucleoside analog pro-drugs processed by pyrimidine metabolism into a deoxynucleotide analog that depletes the key epigenetic regulator DNA methyltranseferase 1 (DNMT1). Here, upon serial analyses of DNMT1 levels in patients' bone marrows on-therapy, we found DNMT1 was not depleted at relapse. Showing why, bone marrows at relapse exhibited shifts in expression of key pyrimidine metabolism enzymes in directions adverse to pro-drug activation. Further investigation revealed the origin of these shifts. Pyrimidine metabolism is a network that senses and regulates deoxynucleotide amounts. Deoxynucleotide amounts were disturbed by single exposures to decitabine or 5-azacytidine, via off-target depletion of thymidylate synthase and ribonucleotide reductase respectively. Compensating pyrimidine metabolism shifts peaked 72-96 h later. Continuous pro-drug exposures stabilized these adaptive metabolic responses to thereby prevent DNMT1-depletion and permit exponential leukemia out-growth as soon as day 40. The consistency of the acute metabolic responses enabled exploitation: simple treatment modifications in xenotransplant models of chemorefractory leukemia extended noncytotoxic DNMT1-depletion and leukemia control by several months. In sum, resistance to decitabine and 5-azacytidine originates from adaptive responses of the pyrimidine metabolism network; these responses can be anticipated and thus exploited.
Topics: Animals; Antimetabolites, Antineoplastic; Azacitidine; Cell Line, Tumor; DNA (Cytosine-5-)-Methyltransferase 1; DNA Methylation; Decitabine; Disease Models, Animal; Dose-Response Relationship, Drug; Drug Resistance, Neoplasm; Humans; Metabolic Networks and Pathways; Mice; Pyrimidines; Uridine Kinase
PubMed: 32770088
DOI: 10.1038/s41375-020-1003-x -
Molecules (Basel, Switzerland) Jan 2023The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four...
The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e.
Topics: Molecular Dynamics Simulation; p21-Activated Kinases; Pyrimidines; Protein Kinase Inhibitors; Molecular Docking Simulation; Structure-Activity Relationship
PubMed: 36615619
DOI: 10.3390/molecules28010413 -
The Journal of General Physiology May 1950The distribution of purines and pyrimidines in desoxypentose nucleic acids prepared from a variety of animal and plant sources has been studied. 1. The nucleic acids...
The distribution of purines and pyrimidines in desoxypentose nucleic acids prepared from a variety of animal and plant sources has been studied. 1. The nucleic acids were prepared from calf thymus, calf kidney, sheep spleen, horse spleen, chicken erythrocyte, turtle erythrocyte, trout sperm, shad testes, sea urchin sperm, wheat germ, and Pneumococcus Type III. 2. Separate hydrolyses were carried out for the determination of purines and pyrimidines. These procedures permitted nearly quantitative recovery of nucleic acid phosphorus in many of the preparations examined. 3. In the case of those preparations where a quantitative recovery was obtained it can be concluded that no bases other than adenine, guanine, thymine, and cytosine were present in appreciable amounts. 4. The distribution of purines and pyrimidines in all the nucleic acids studied renders the tetranucleotide hypothesis untenable. 5. The results of the analyses have indicated no great differences in the composition of these nucleic acids with respect to purines and pyrimidines.
Topics: Adenine; Animals; Cattle; Cytosine; Guanine; Horses; Nucleic Acids; Purines; Pyrimidines; Sheep; Thymine
PubMed: 15422104
DOI: 10.1085/jgp.33.5.497 -
Molecules (Basel, Switzerland) May 2018We report herein a new metal free synthetic pathway to generate tetracyclic compounds from 3-aminothieno[3,2-]pyridine-2-carboxylate. To enlarge the molecular diversity,...
We report herein a new metal free synthetic pathway to generate tetracyclic compounds from 3-aminothieno[3,2-]pyridine-2-carboxylate. To enlarge the molecular diversity, we studied the Suzuki coupling of 9-chloro-6-pyrido[1,2-]pyrido[2',3':4,5]thieno[3,2-]pyrimidin-6-one and several boronic acids were easily introduced.
Topics: Chemistry Techniques, Synthetic; Cyclization; Molecular Structure; Pyridines; Pyrimidines
PubMed: 29751677
DOI: 10.3390/molecules23051159 -
Current Opinion in Structural Biology Feb 2014There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail... (Review)
Review
There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base ionization or tautomerization. These high energy purine-pyrimidine base-pairs include G•C(+) and A•T Hoogsteen base-pairs, which entail ∼180° rotation of the purine base in a Watson-Crick base-pair, protonation of cytosine N3, and constriction of the C1'-C1' distance by ∼2.5Å. Other high energy pure-pyrimidine base-pairs include G•T, G•U, and A•C mispairs that adopt Watson-Crick like geometry through either base ionization or tautomerization. Although difficult to detect and characterize using biophysical methods, high energy purine-pyrimidine base-pairs appear to be more common than once thought. They further expand the structural and functional diversity of canonical and non-canonical nucleic acid base-pairs.
Topics: Animals; Base Pairing; DNA; Humans; Isomerism; Models, Molecular; Nucleic Acid Conformation; Purines; Pyrimidines
PubMed: 24721455
DOI: 10.1016/j.sbi.2013.12.003 -
Biomedicine & Pharmacotherapy =... Dec 2022Novel pyrazolo[3,4-d] pyrimidine derivatives bearing carbon-aryl(heteryl)idene moieties were synthesized via a condensation reaction of 5-aminopyrazoles and cyclic...
Novel pyrazolo[3,4-d] pyrimidine derivatives bearing carbon-aryl(heteryl)idene moieties were synthesized via a condensation reaction of 5-aminopyrazoles and cyclic lactams. The preparation of the target compounds employed bioisosterism, where a pyrazole ring was a major replacement. Fifteen target compounds were investigated for their antiproliferative activity on five human cancer cell lines; derivative (E)- 1-methyl-9-(3,4,5-trimethoxybenzylidene)- 6,7,8,9-tetrahydropyrazolo[3,4-d]pyrido[1,2-a]pyrimidin-4(1H)-one (10k) showed the highest activity (IC value (0.03-1.6 μM), on selected cell lines. Results of an in vivo experiment on an HT-29 xenograft nude mouse model also confirmed that 10k inhibited tumor growth. The proposed anticancer mechanism of 10k in HT-29 and HCT-116 cells was that 10k caused G2/M phase arrest in cancer cells and decreased the mitochondrial membrane potential (Δψmt). Additional studies were conducted on HUVEC, where 10k significantly inhibited HUVEC cell migration, adhesion, and tube formation activity. Molecular modeling studies revealed that 10k forms hydrogen bonds with cys-919 of vascular endothelial growth factor receptor 2 (VEGFR-2) and inhibit VEGFR-2 kinase activity. Moreover, tubulin polymerization assay results showed that 10k formed hydrogen bonds with Asn-101 and Gln-11 of tubulin. Furthermore, it could change the aberration of microtubule arrangements in HUVEC and inhibit tubulin polymerization. These results indicate that the main anticancer activity of 10k may be mediated by anti-vascular effects and inhibition of tubulin polymerization in pre-clinical trials.
Topics: Mice; Animals; Humans; Pyrimidines; Vascular Endothelial Growth Factor Receptor-2; Tubulin; Vascular Endothelial Growth Factor A; Structure-Activity Relationship; Antineoplastic Agents
PubMed: 36411633
DOI: 10.1016/j.biopha.2022.113948 -
Journal of Molecular and Cellular... Feb 2018Pathologically increased activity of Ca/calmodulin-dependent protein kinase II (CaMKII) and the associated Ca-leak from the sarcoplasmic reticulum are recognized to be...
OBJECTIVE
Pathologically increased activity of Ca/calmodulin-dependent protein kinase II (CaMKII) and the associated Ca-leak from the sarcoplasmic reticulum are recognized to be important novel pharmacotherapeutic targets in heart failure and cardiac arrhythmias. However, CaMKII-inhibitory compounds for therapeutic use are still lacking. We now report on the cellular and molecular effects of a novel pyrimidine-based CaMKII inhibitor developed towards clinical use.
METHODS AND RESULTS
Our findings demonstrate that AS105 is a high-affinity ATP-competitive CaMKII-inhibitor that by its mode of action is also effective against autophosphorylated CaMKII (in contrast to the commonly used allosteric CaMKII-inhibitor KN-93). In isolated atrial cardiomyocytes from human donors and ventricular myocytes from CaMKIIδ-overexpressing mice with heart failure, AS105 effectively reduced diastolic SR Ca leak by 38% to 65% as measured by Ca-sparks or tetracaine-sensitive shift in [Ca]. Consistent with this, we found that AS105 suppressed arrhythmogenic spontaneous cardiomyocyte Ca-release (by 53%). Also, the ability of the SR to accumulate Ca was enhanced by AS105, as indicated by improved post-rest potentiation of Ca-transient amplitudes and increased SR Ca-content in the murine cells. Accordingly, these cells had improved systolic Ca-transient amplitudes and contractility during basal stimulation. Importantly, CaMKII inhibition did not compromise systolic fractional Ca-release, diastolic SR Ca-reuptake via SERCA2a or Ca-extrusion via NCX.
CONCLUSION
AS105 is a novel, highly potent ATP-competitive CaMKII inhibitor. In vitro, it effectively reduced SR Ca-leak, thus improving SR Ca-accumulation and reducing cellular arrhythmogenic correlates, without negatively influencing excitation-contraction coupling. These findings further validate CaMKII as a key target in cardiovascular disease, implicated by genetic, allosteric inhibitors, and pseudo-substrate inhibitors.
Topics: Animals; Calcium; Calcium Channels, L-Type; Calcium-Calmodulin-Dependent Protein Kinase Type 2; Excitation Contraction Coupling; Humans; Mice, Inbred C57BL; Myocytes, Cardiac; Protein Kinase Inhibitors; Pyrimidines; Sarcoplasmic Reticulum
PubMed: 29294328
DOI: 10.1016/j.yjmcc.2017.12.015