-
Journal of Bacteriology Nov 1961Løvtrup, Søren (University of Göteborg, Sweden) and David Shugar. Utilization of pyrimidines and pyrimidine deoxynucleosides by Thermobacterium acidophilum...
Løvtrup, Søren (University of Göteborg, Sweden) and David Shugar. Utilization of pyrimidines and pyrimidine deoxynucleosides by Thermobacterium acidophilum (Lactobacillus acid-ophilus). J. Bacteriol. 82:623-631. 1961.-The utilization of pyrimidine deoxynucleosides was investigated by means of deoxyribosides of unnatural pyrimidines, especially by halogen-substituted uracil derivatives. All investigated deoxyribosides could be used, except that of N-methylthymidine. It was concluded that this substance cannot be a substrate for the enzyme trans-N-deoxyribosylase, which has been shown to be active in the utilization of deoxyribosides in this microorganism. With uracil as the only pyrimidine source, the halogen-substituted deoxyuridines had a certain inhibitory effect on growth. Contrary to previous findings, it was observed that normal growth occurs in the presence of thymine as the only pyrimidine source. The utilization of this substance is less efficient than that of uracil; a 1:10 dilution leads to a decrease in the extent of growth with the former, but not with the latter. From these results, complemented with experiments in which halogen-substituted uracil derivatives and the corresponding ribosides or deoxyribosides were used as inhibitors, it has been possible to account for most of the metabolic interconversions of pyrimidines in the investigated microorganism.
Topics: Lactobacillus; Lactobacillus acidophilus; Nucleosides; Nucleotides; Pentosyltransferases; Pyrimidines; Sweden; Thymidine; Thymine; Uracil
PubMed: 14466913
DOI: 10.1128/jb.82.5.623-631.1961 -
Chemical & Pharmaceutical Bulletin 2014A series of diarylureas and diarylamides possessing pyrrolo[2,3-d]pyrimidine scaffold was designed and synthesized. The in vitro antiproliferative activities of a...
A series of diarylureas and diarylamides possessing pyrrolo[2,3-d]pyrimidine scaffold was designed and synthesized. The in vitro antiproliferative activities of a selected group of the target compounds against NCI-60 cell line panel were tested and compared with Sorafenib and Imatinib as reference compounds. Most of the compounds showed strong and broad-spectrum antiproliferative activities. Compounds IVa, IVb, and IVd with benzamido moiety at position 4 of the pyrrolo[2,3-d]pyrimidine nucleus, para-disubstituted phenyl ring at N1-position of pyrrolo[2,3-d]pyrimidine scaffold, and urea linker showed strong and broad-spectrum anticancer results with high potencies and efficacies. In addition, the amide derivatives Vb and Vc demonstrated one-digit nanomolar IC50 values over two and one cell line(s), respectively. Amid all the target compounds, compound IVa demonstrated the best results in both one-dose and five-dose testing modes. It showed 109.18% mean % inhibition over the NCI-60 cancer cell line panel at 10 µM concentration, submicromolar 50% inhibitory concentration (IC50) values over eight cell lines of eight different cancer types, and high efficacy with total growth inhibition (TGI) and 50% lethal concentration (LC50) values less than 4.22 µM over three colon, ovarian, and prostate cancer cell lines. It showed superior potency and efficacy to Sorafenib and Imatinib over most of the tested cell lines.
Topics: Antineoplastic Agents; Benzamides; Cell Line, Tumor; Drug Screening Assays, Antitumor; Humans; Imatinib Mesylate; Niacinamide; Phenylurea Compounds; Piperazines; Pyrimidines; Pyrroles; Sorafenib
PubMed: 24390490
DOI: 10.1248/cpb.c13-00249 -
RNA (New York, N.Y.) May 2017Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites....
Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.
Topics: Base Pairing; Cytosine; Databases, Nucleic Acid; Nucleic Acid Conformation; Pyrimidines; RNA, Viral; Thermodynamics; Uracil
PubMed: 28213527
DOI: 10.1261/rna.059865.116 -
Bioorganic & Medicinal Chemistry Jan 2021A series of methoxy naphthyl substituted cyclopenta[d]pyrimidine compounds, 4-10, were designed and synthesized to study the influence of the 3-D conformation on...
A series of methoxy naphthyl substituted cyclopenta[d]pyrimidine compounds, 4-10, were designed and synthesized to study the influence of the 3-D conformation on microtubule depolymerizing and antiproliferative activities. NOESY studies with the N,2-dimethyl-N-(6'-methoxynaphthyl-1'-amino)-cyclopenta[d]pyrimidin-4-amine (4) showed hindered rotation of the naphthyl ring around the cyclopenta[d]pyrimidine scaffold. In contrast, NOESY studies with N,2-dimethyl-N-(5'-methoxynaphthyl-2'-amino)-cyclopenta[d]pyrimidin-4-amine (5) showed free rotation of the naphthyl ring around the cyclopenta[d]pyrimidine scaffold. The rotational flexibility and conformational dissimilarity between 4 and 5 led to a significant difference in biological activities. Compound 4 is inactive while 5 is the most potent in this series with potent microtubule depolymerizing effects and low nanomolar IC values in vitro against a variety of cancer cell lines. The ability of 5 to inhibit tumor growth in vivo was investigated in a U251 glioma xenograft model. The results show that 5 had better antitumor effects than the positive control temozolomide and have identified 5 as a potential preclinical candidate for further studies. The influence of conformation on the microtubule depolymerizing and antitumor activity forms the basis for the development of conformation-activity relationships for the cyclopenta[d]pyrimidine class of microtubule targeting agents.
Topics: Animals; Antineoplastic Agents; Brain Neoplasms; Cell Proliferation; Cyclopentanes; Dose-Response Relationship, Drug; Drug Screening Assays, Antitumor; Female; Glioma; Humans; Male; Mice; Mice, Nude; Microtubules; Models, Molecular; Molecular Conformation; Neoplasms, Experimental; Pyrimidines; Structure-Activity Relationship; Tumor Cells, Cultured
PubMed: 33310545
DOI: 10.1016/j.bmc.2020.115887 -
The Journal of Biological Chemistry Apr 2012Protozoan parasites of the Leishmania genus express the metabolic machinery to synthesize pyrimidine nucleotides via both de novo and salvage pathways. To evaluate the...
Protozoan parasites of the Leishmania genus express the metabolic machinery to synthesize pyrimidine nucleotides via both de novo and salvage pathways. To evaluate the relative contributions of pyrimidine biosynthesis and salvage to pyrimidine homeostasis in both life cycle stages of Leishmania donovani, individual mutant lines deficient in either carbamoyl phosphate synthetase (CPS), the first enzyme in pyrimidine biosynthesis, uracil phosphoribosyltransferase (UPRT), a salvage enzyme, or both CPS and UPRT were constructed. The Δcps lesion conferred pyrimidine auxotrophy and a growth requirement for medium supplementation with one of a plethora of pyrimidine nucleosides or nucleobases, although only dihydroorotate or orotate could circumvent the pyrimidine auxotrophy of the Δcps/Δuprt double knockout. The Δuprt null mutant was prototrophic for pyrimidines but could not salvage uracil or any pyrimidine nucleoside. The capability of the Δcps parasites to infect mice was somewhat diminished but still robust, indicating active pyrimidine salvage by the amastigote form of the parasite, but the Δcps/Δuprt mutant was completely attenuated with no persistent parasites detected after a 4-week infection. Complementation of the Δcps/Δuprt clone with either CPS or UPRT restored infectivity. These data establish that an intact pyrimidine biosynthesis pathway is essential for the growth of the promastigote form of L. donovani in culture, that all uracil and pyrimidine nucleoside salvage in the parasite is mediated by UPRT, and that both the biosynthetic and salvage pathways contribute to a robust infection of the mammalian host by the amastigote. These findings impact potential therapeutic design and vaccine strategies for visceral leishmaniasis.
Topics: Animals; Carbamoyl-Phosphate Synthase (Ammonia); Female; Homeostasis; Leishmania donovani; Leishmaniasis Vaccines; Leishmaniasis, Visceral; Macrophages, Peritoneal; Mice; Mice, Inbred BALB C; Molecular Sequence Data; Pentosyltransferases; Phosphorylation; Pyrimidines; Uracil; Uridine
PubMed: 22367196
DOI: 10.1074/jbc.M112.346502 -
Medecine Sciences : M/S Jan 2015RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, hepatitis C or measles. They also represent an emerging threat because of increased... (Review)
Review
RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, hepatitis C or measles. They also represent an emerging threat because of increased worldwide exchanges and human populations penetrating more and more natural ecosystems. Recent progresses in our understanding of cellular pathways controlling viral replication suggest that compounds targeting host cell functions, rather than the virus itself, could inhibit a large panel of RNA viruses. In particular, several academic laboratories and private companies are now seeking molecules that stimulate the host innate antiviral response. One appealing strategy is to identify molecules that induce the large cluster of antiviral genes known as Interferon-Stimulated Genes (ISGs). To reach this goal, we have developed a phenotypic assay based on human cells transfected with a luciferase reporter gene under control of an interferon-stimulated response element (ISRE). This system was used in a high-throughput screening of chemical libraries comprising around 54,000 compounds. Among validated hits, compound DD264 was shown to boost the innate immune response in cell cultures, and displayed a broad-spectrum antiviral activity. While deciphering its mode of action, DD264 was found to target the fourth enzyme of de novo pyrimidine biosynthesis, namely the dihydroorotate dehydrogenase (DHODH). Thus, our data unraveled a yet unsuspected link between pyrimidine biosynthesis and the innate antiviral response.
Topics: Antiviral Agents; Dihydroorotate Dehydrogenase; Drug Evaluation, Preclinical; Enzyme Inhibitors; High-Throughput Screening Assays; Humans; Immunity, Innate; Oxidoreductases Acting on CH-CH Group Donors; Phenotype; Pyrimidines; Small Molecule Libraries; Viruses
PubMed: 25658737
DOI: 10.1051/medsci/20153101019 -
The Journal of Experimental Medicine Mar 1985We have found that the anaerobic protozoan parasite Giardia lamblia is incapable of de novo pyrimidine metabolism, as shown by its inability to incorporate orotate,...
We have found that the anaerobic protozoan parasite Giardia lamblia is incapable of de novo pyrimidine metabolism, as shown by its inability to incorporate orotate, bicarbonate, and aspartate into the pyrimidine nucleotide pool. Results from high performance liquid chromatography of pyrimidine and pyrimidine nucleoside pulse-labeled nucleotide pools and enzyme assays suggest that the parasite satisfies its pyrimidine nucleotide needs predominantly through salvage of uracil by a cytoplasmic uracil phosphoribosyltransferase. Exogenous uridine and cytidine are primarily converted to uracil by the action of uridine hydrolase and cytidine deaminase before incorporation into nucleotide pools. Direct salvage of cytosine occurs to a relatively limited extent via cytosine phosphoribosyltransferase. G. lamblia relies on salvage of exogenous thymidine for ribosylthymine monophosphate (TMP) synthesis, accomplished primarily through the action of a 100,000 g-pelletable thymidine phosphotransferase.
Topics: Animals; Chromatography, High Pressure Liquid; Cytidine; Giardia; Pentosyltransferases; Pyrimidine Nucleosides; Pyrimidines; Thymidine; Uridine
PubMed: 3973534
DOI: 10.1084/jem.161.3.437 -
Chemical & Pharmaceutical Bulletin 2018Phosphodiesterase (PDE) 10A is a dual hydrolase of cAMP and cGMP and highly expressed in striatal medium spiny neurons. Inhibition of PDE10A modulates the activity of...
Discovery of 2-[(E)-2-(7-Fluoro-3-methylquinoxalin-2-yl)vinyl]-6-pyrrolidin-1-yl-N-(tetrahydro-2H-pyran-4-yl)pyrimidin-4-amine Hydrochloride as a Highly Selective PDE10A Inhibitor.
Phosphodiesterase (PDE) 10A is a dual hydrolase of cAMP and cGMP and highly expressed in striatal medium spiny neurons. Inhibition of PDE10A modulates the activity of medium spiny neurons (MSN) via the regulation of cAMP and cGMP. Signal control of MSN is considered associated with psychotic symptoms. Therefore PDE10A inhibitor is expected as a therapeutic method for psychosis disease such as schizophrenia. Avanafil (1) is a PDE5 inhibitor (treatment for erectile dysfunction) discovered by our company. We paid attention to the homology of PDE10A and PDE5 and took advantage of PDE5 inhibitor library to discover PDE10A inhibitors, and found a series of compounds that exhibit higher potency for PDE10A than PDE5. We transformed the afforded derivatives, which had weak inhibitory activity against PDE10A, and discovered stilbene as a PDE10A inhibitor. Brain penetration of this compound was improved by further conversion of N-containing heterocycles and their substituents. The afforded dimethylaminopyrimidine was effective for rat conditioned avoidance response (CAR) test; however, it did not exhibit good brain penetration. We performed in-depth optimization focusing on substituents of the quinoxaline ring, and produced 3-methyl-7-fluoro quinoxaline. This compound was the most effective in rat CAR test due to its strong PDE10A inhibitory activity and good pharmacokinetics.
Topics: Animals; Avoidance Learning; Binding Sites; Crystallography, X-Ray; Drug Evaluation, Preclinical; Inhibitory Concentration 50; Molecular Dynamics Simulation; Phosphodiesterase Inhibitors; Phosphoric Diester Hydrolases; Pyrimidines; Quinoxalines; Rats; Structure-Activity Relationship
PubMed: 29491258
DOI: 10.1248/cpb.c17-00783 -
Nuclear Medicine and Biology Oct 2016Chemokine receptor-4 (CXCR4, fusin, CD184) is expressed on several tissues involved in immune regulation and is upregulated in many diseases including malignant gliomas....
INTRODUCTION
Chemokine receptor-4 (CXCR4, fusin, CD184) is expressed on several tissues involved in immune regulation and is upregulated in many diseases including malignant gliomas. A radiolabeled small molecule that readily crosses the blood-brain barrier can aid in identifying CXCR4-expressing gliomas and monitoring CXCR4-targeted therapy. In the current work, we have synthesized and evaluated an [(18)F]-labeled small molecule based on a pyrimidine-pyridine amine for its ability to target CXCR4.
EXPERIMENTAL
The nonradioactive standards and the nitro precursor used in this study were prepared using established methods. An HPLC method was developed to separate the nitro-precursor from the nonradioactive standard and radioactive product. The nitro-precursor was radiolabeled with (18)F under inert, anhydrous conditions using the [(18)F]-kryptofix 2.2.2 complex to form the desired N-(4-(((6-[(18)F]fluoropyridin-2-yl)amino)methyl)benzyl)pyrimidin-2-amine ([(18)F]-3). The purified radiolabeled compound was used in serum stability, partition coefficient, cellular uptake, and in vivo cancer targeting studies.
RESULTS
[(18)F]-3 was synthesized in 4-10% decay-corrected yield (to start of synthesis). [(18)F]-3 (tR ≈ 27 min) was separated from the precursor (tR ≈ 30 min) using a pentafluorophenyl column with an isocratic solvent system. [(18)F]-3 displayed acceptable serum stability over 2 h. The amount of [(18)F]-3 bound to the plasma proteins was determined to be > 97%. The partition coefficient (LogD7.4) is 1.4 ± 0.5. Competitive in vitro inhibition indicated 3 does not inhibit uptake of (67)Ga-pentixafor. Cell culture media incubation and ex vivo urine analysis indicate rapid metabolism of [(18)F]-3 into hydrophilic metabolites. Thus, in vitro uptake of [(18)F]-3 in CXCR4 overexpressing U87 cells (U87 CXCR4) and U87 WT indicated no specific binding. In vivo studies in mice bearing U87 CXCR4 and U87 WT tumors on the left and right shoulders were carried out using [(18)F]-3 and (68)Ga-pentixafor on consecutive days. The CXCR4 positive tumor was clearly visualized in the PET study using (68)Ga-pentixafor, but not with [(18)F]-3.
CONCLUSIONS
We have successfully synthesized both a radiolabeled analog to previously reported CXCR4-targeting molecules and a nitro precursor. Our in vitro and in vivo studies indicate that [(18)F]-3 is rapidly metabolized and, therefore, does not target CXCR4-expressing tumors. Optimization of the structure to improve the in vivo (and in vitro) stability, binding, and solubility could lead to an appropriate CXCR4-targeted radiodiagnositic molecule.
Topics: Amines; Animals; Biological Transport; Cell Line, Tumor; Chemistry Techniques, Synthetic; Drug Stability; Fluorine Radioisotopes; Glioma; Halogenation; Humans; Isotope Labeling; Male; Mice; Positron Emission Tomography Computed Tomography; Pyridines; Pyrimidines; Radiochemistry; Receptors, CXCR4
PubMed: 27485481
DOI: 10.1016/j.nucmedbio.2016.05.005 -
Journal of Enzyme Inhibition and... Dec 2018Three series of 2-arylpyridothieno[3,2-d]pyrimidin-4-ones 3a-j, pyridothienotriazolopyrimidines 6-8 and 4-imino-pyridothieno[3,2-d]pyrimidines 9a,b were prepared to...
Three series of 2-arylpyridothieno[3,2-d]pyrimidin-4-ones 3a-j, pyridothienotriazolopyrimidines 6-8 and 4-imino-pyridothieno[3,2-d]pyrimidines 9a,b were prepared to improve the pim-1 inhibitory activity of the previously reported 2-arylpyridothieno[3,2-d]pyrimidin-4-ones. All the test compounds showed highly potent pim-1 inhibition with IC in the range of 0.06-1.76 µM. No significant difference was detected between the pim-1 inhibitory activity of the 4-pyrimidinone and the 4-imino (=NH) or the cyclised triazolopyrimidine derivatives. The most active compounds were tested for their cytotoxic activity on MCF7 and HCT116 and showed potent activity on both the cell lines.
Topics: Antineoplastic Agents; Cell Proliferation; Dose-Response Relationship, Drug; Drug Screening Assays, Antitumor; Humans; Molecular Structure; Protein Kinase Inhibitors; Proto-Oncogene Proteins c-pim-1; Pyrimidines; Pyrimidinones; Structure-Activity Relationship; Tumor Cells, Cultured
PubMed: 29161928
DOI: 10.1080/14756366.2017.1389921