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Methods (San Diego, Calif.) May 1999Single-atom substitution experiments provide atomic resolution biochemical information concerning RNA structure and function. Traditionally, these experiments are...
Single-atom substitution experiments provide atomic resolution biochemical information concerning RNA structure and function. Traditionally, these experiments are performed using chimeric RNAs generated by reassembly of full-length RNA from a synthetic substituted oligonucleotide and a truncated RNA transcript. Unfortunately, this technique is limited by the technical difficulty of assembling and measuring the effect of each singly substituted molecule in a given RNA. Here we review an alternate method for rapidly screening the effect of chemical group substitutions on RNA function. Nucleotide analog interference mapping is a chemogenetic approach that utilizes a series 5'-O-(1-thio)-nucleoside analog triphosphates to simultaneously, yet individually, probe the contribution of a functional group at every nucleotide position in an RNA molecule. A population of randomly substituted RNAs is prepared by including phosphorothioate-tagged nucleotide analogs in an in vitro transcription reaction. The active molecules in the RNA population are selected by an activity assay, and the location of the analog substitution detrimental to activity is identified by cleavage at the phosphorothioate tag with iodine and resolution of the cleavage fragments by gel electrophoresis. This method, which is as easy as RNA sequencing, is applicable to any RNA that can be transcribed in vitro and has an assayable function. Here we describe protocols for the synthesis of phosphorothioate-tagged analogs and their incorporation into RNA transcripts. The incorporation properties and unique biochemical signatures of each individual analog are discussed.
Topics: Adenosine; Guanosine; Models, Chemical; Models, Genetic; Nucleotide Mapping; Phosphorus; Pyrimidines; RNA; Thionucleotides; Transcription, Genetic
PubMed: 10208815
DOI: 10.1006/meth.1999.0755 -
The Journal of Toxicological Sciences 2009Congenital disorders of metabolism show a wide spectrum of symptoms as a consequence of impairment of a certain metabolic pathway by mutated enzymes resulting in... (Review)
Review
Children's toxicology from bench to bed--Liver injury (1): Drug-induced metabolic disturbance--toxicity of 5-FU for pyrimidine metabolic disorders and pivalic acid for carnitine metabolism.
Congenital disorders of metabolism show a wide spectrum of symptoms as a consequence of impairment of a certain metabolic pathway by mutated enzymes resulting in abnormal accumulation of enzyme substrates, deficiency of expected products, and abnormal burden to collateral metabolic pathways, etc. However, in some occasions, depending on which pathway up to what degree of disturbance, it can be asymptomatic until a certain kind of burden is placed on to the patient. Enzyme deficiency involved in pyrimidine degradation, such as Dihydropyrimidine dehydrogenase (DPD) and Dihydropyrimidinase (DHP), has been reported with convulsion or autism as symptoms, but many asymptomatic cases are also reported. However, when the patients are treated with 5-fluorouracil, a pyrimidine analogue anticancer drug, lethal side-effects can be seen even in asymptomatic patients. Some oral cephem antibiotics have pivalic acid side chain to increase absorption rate at intestine. These antibiotics degrade into active antibiotics and pivalic acid at the intestinal wall. This pivalic acid is carnitine-conjugated and excreted into urine. Carnitine acts as a carrier of long chain fatty acid to mitochondria and to beta-oxidation, thus an important molecule for energy production by beta-oxidation and maintenance of mitochondrial function. Because of this, long term administration of such antibiotics could induce depletion of carnitine from the body and lead to low ketotic hypoglycemia, convulsion and consciousness disturbance. This paper reports some possible serious side effects closely linked to drug metabolism.
Topics: Amidohydrolases; Animals; Anti-Bacterial Agents; Antineoplastic Agents; Carnitine; Cephalosporins; Child; Dihydropyrimidine Dehydrogenase Deficiency; Female; Fluorouracil; Humans; Intestinal Absorption; Pentanoic Acids; Purine-Pyrimidine Metabolism, Inborn Errors; Pyrimidines; Rats
PubMed: 19571472
DOI: 10.2131/jts.34.sp217 -
Drug Design, Development and Therapy 2017In our efforts to address the rising incidence of hepatocellular carcinoma (HCC), we have made a commitment to the synthesis of novel molecules to combat Hep-G2 cells. A...
-TSA-promoted syntheses of 5H-benzo[h] thiazolo[2,3-b]quinazoline and indeno[1,2-d] thiazolo[3,2-a]pyrimidine analogs: molecular modeling and in vitro antitumor activity against hepatocellular carcinoma.
In our efforts to address the rising incidence of hepatocellular carcinoma (HCC), we have made a commitment to the synthesis of novel molecules to combat Hep-G2 cells. A facile and highly efficient one-pot, multicomponent reaction has been successfully devised utilizing a -toluenesulfonic acid (-TSA)-catalyzed domino Knoevenagel/Michael/intramolecular cyclization approach for the synthesis of novel 5H-benzo[h]thiazolo[2,3-b]quinazoline and indeno[1,2-d] thiazolo[3,2-a]pyrimidine analogs bearing a bridgehead nitrogen atom. This domino protocol constructed one new ring by the concomitant formation of multiple bonds (C-C, C-N, and C=N) involving multiple steps without the use of any metal catalysts in one-pot, with all reactants effi-ciently exploited. All the newly synthesized compounds were authenticated by means of Fourier transform infrared spectroscopy, liquid chromatography-mass spectrometry, proton nuclear magnetic resonance spectroscopy, and carbon-13 nuclear magnetic resonance spectroscopy, together with elemental analysis, and their antitumor activity was evaluated in vitro on a Hep-G2 human cancer cell line by sulforhodamine B assay. Computational molecular modeling studies were carried out on cancer-related targets, including interleukin-2, interleukin-6, Caspase-3, and Caspase-8. Two compounds (4A and 6A) showed growth inhibitory activity comparable to the positive control Adriamycin, with growth inhibition of 50% <10 μg/mL. The results of the comprehensive structure-activity relationship study confirmed the assumption that two or more electronegative groups on the phenyl ring attached to the thiazolo[2,3-b]quinazoline system showed the optimum effect. The in silico simulations suggested crucial hydrogen bond and π-π stacking interactions, with a good ADMET (absorption, distribution, metabolism, excretion, and toxicity) profile and molecular dynamics, in order to explore the molecular targets of HCC which were in complete agreement with the in vitro findings. Considering their significant anticancer activity, 4A and 6A are potential drug candidates for the management of HCC.
Topics: Antineoplastic Agents; Benzenesulfonates; Carbon-13 Magnetic Resonance Spectroscopy; Carcinoma, Hepatocellular; Cell Proliferation; Chromatography, Liquid; Dose-Response Relationship, Drug; Drug Design; Hep G2 Cells; Humans; Liver Neoplasms; Mass Spectrometry; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular Structure; Proton Magnetic Resonance Spectroscopy; Pyrimidines; Quinazolines; Spectroscopy, Fourier Transform Infrared; Structure-Activity Relationship
PubMed: 28615927
DOI: 10.2147/DDDT.S136692 -
PloS One 2018Purine and pyrimidine analogues have important uses in chemotherapies against cancer, and a better understanding of the mechanisms that cause resistance to these drugs...
Purine and pyrimidine analogues have important uses in chemotherapies against cancer, and a better understanding of the mechanisms that cause resistance to these drugs is therefore of importance in cancer treatment. In the yeast Saccharomyces cerevisiae, overexpression of the HAM1 gene encoding inosine triphosphate pyrophosphatase confers resistance to both the purine analogue 6-N-hydroxylaminopurine (HAP) and the pyrimidine analogue 5-fluorouracil (5-FU) (Carlsson et al., 2013, PLoS One 8, e52094). To find out more about the mechanisms of resistance to nucleotide analogues, and possible interdependencies between purine and pyrimidine analogue resistance mechanisms, we screened a plasmid library in yeast for genes that confer HAP resistance when overexpressed. We cloned four such genes: ADE4, DUT1, APT2, and ATR1. We further looked for genetic interactions between these genes and genes previously found to confer resistance to 5-FU. We found that HMS1, LOG1 (YJL055W), HAM1, and ATR1 confer resistance to both 5-FU and HAP, whereas ADE4, DUT1 and APT2 are specific for HAP resistance, and CPA1 and CPA2 specific for 5-FU resistance. Possible mechanisms for 5-FU and HAP detoxification are discussed based on the observed genetic interactions. Based on the effect of LOG1 against both 5-FU and HAP toxicity, we propose that the original function of the LOG (LONELY GUY) family of proteins likely was to degrade non-canonical nucleotides, and that their role in cytokinin production is a later development in some organisms.
Topics: Adenine; Antimetabolites; Cloning, Molecular; Drug Resistance, Fungal; Fluorouracil; Fungal Proteins; Gene Dosage; Gene Expression Regulation, Fungal; Gene Knockout Techniques; Genes, Fungal; Inactivation, Metabolic; Purines; Pyrimidines; Recombinant Proteins; Saccharomyces cerevisiae Proteins; Substrate Specificity
PubMed: 29738539
DOI: 10.1371/journal.pone.0196840 -
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 -
Zeitschrift Fur Naturforschung. C,... 2007The pyrrole derivatives la, b and 2a, b were used as precursors for the preparation of N-substituted pyrrole derivatives 3a, b-9a, b and pyrrolo[2,3-d]pyrimidines 13-16....
The pyrrole derivatives la, b and 2a, b were used as precursors for the preparation of N-substituted pyrrole derivatives 3a, b-9a, b and pyrrolo[2,3-d]pyrimidines 13-16. Also, all the newly prepared products were tested for anti-inflammatory activity as analogues to fenamates, and some of them revealed moderate anti-inflammatory activity compared to the standard drug indomethacin.
Topics: Animals; Anti-Inflammatory Agents, Non-Steroidal; Indomethacin; Models, Molecular; Molecular Structure; Pyrimidines; Pyrroles; Rats
PubMed: 17425101
DOI: 10.1515/znc-2007-1-205 -
Chemical Biology & Drug Design Jan 2021Non-nucleoside reverse transcriptase inhibitors (NNRTIs) inhibit reverse transcription and block the replication of HIV-1. Currently, NNRTIs are usually used as part of...
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) inhibit reverse transcription and block the replication of HIV-1. Currently, NNRTIs are usually used as part of a three-drug combination given to patients as antiretroviral therapy. These combinations involve other classes of anti-HIV-1 drugs, commonly nucleoside reverse transcriptase inhibitors (NRTIs). However, attempts are being made to develop two-drug maintenance therapies, some of which involve an NNRTI and an integrase strand transfer inhibitor. This has led to a renewed interest in developing novel NNRTIs, with a major emphasis on designing compounds that can effectively inhibit the known NNRTI-resistant mutants. We have generated and tested novel rilpivirine (RPV) analogs. The new compounds were designed to exploit a small opening in the upper right periphery of the NNRTI-binding pocket. The best of the new compounds, 12, was a more potent inhibitor of the NNRTI-resistant mutants we tested than either doravirine or efavirenz but was inferior to RPV. We describe the limitations on the modifications that can be appended to the "upper right side" of the RPV core and the effects of substituting other cores for the central pyrimidine core of RPV and make suggestions about how this information can be used in NNRTI design.
Topics: Anti-HIV Agents; Binding Sites; Drug Design; Drug Resistance, Viral; HIV Infections; HIV Reverse Transcriptase; HIV-1; Humans; Molecular Dynamics Simulation; Mutation; Pyridones; Pyrimidines; Rilpivirine; Triazoles
PubMed: 32743937
DOI: 10.1111/cbdd.13766 -
The Journal of Biological Chemistry May 1979Leishmania donovani and Leishmania braziliensis grown in culture formed millimolar concentrations of allopurinol ribonucleoside 5'-monophosphate from [6-14C]allopurinol.... (Comparative Study)
Comparative Study
Leishmania donovani and Leishmania braziliensis grown in culture formed millimolar concentrations of allopurinol ribonucleoside 5'-monophosphate from [6-14C]allopurinol. In addition, allopurinol 1-ribonucleoside, oxipurinol riboside 5'-monophosphate, and three new metabolites of allopurinol, namely, 4-aminopyrazolo(3,4-d)pyrimidine ribonucleoside 5'-monophosphate and the corresponding di- and triphosphates (1-ribosyl 4-aminopyrazolo(3,4-d)pyrimidine 5'-diphosphate and 1-ribosyl 4-aminopyrazolo(3,4-d)pyrimidine 5'-triphosphate) were identified in the parasitic cells. They were formed via a unique amination reaction from 1-ribosyl allopurinol 5'-phosphate, analogous to the conversion of IMP to AMP. [6-14C]Allopurinol was incorporated into RNA of L. donovani in the form of 4-aminopyrazolo(3,4-d)pyrimidine. Adenine reversed the growth inhibition of allopurinol and prevented its metabolism to all of the ribonucleotide metabolites. L. donovani was 2- to 4-fold more active in its metabolism of allopurinol to ribonucleotides than L. braziliensis. 4-Aminopyrazolo(3,4-d)pyrimidine inhibited cell growth and resulted in high intracellular levels of 1-ribosyl allopurinol 5'-phosphate and smaller amounts of the 4-aminopyrazolo(3,4-d)pyrimidine ribonucleotides. The metabolism of allopurinol to 4-aminopyrazolo(3,4-d)pyrimidine ribonucleotides and its resultant cytotoxicity occurs in these parasitic protozoans, but not in mammalian cells.
Topics: Adenine; Allopurinol; Chromatography, High Pressure Liquid; Leishmania; Oxypurinol; Pyrimidines; Ribonucleosides; Ribonucleotides; Species Specificity
PubMed: 438170
DOI: No ID Found -
Molecules (Basel, Switzerland) Feb 2023Upregulated CXCR2 signalling is found in numerous inflammatory, autoimmune and neurodegenerative diseases, as well as in cancer. Consequently, CXCR2 antagonism is a...
Upregulated CXCR2 signalling is found in numerous inflammatory, autoimmune and neurodegenerative diseases, as well as in cancer. Consequently, CXCR2 antagonism is a promising therapeutic strategy for treatment of these disorders. We previously identified, via scaffold hopping, a pyrido[3,4-]pyrimidine analogue as a promising CXCR2 antagonist with an IC value of 0.11 µM in a kinetic fluorescence-based calcium mobilization assay. This study aims at exploring the structure-activity relationship (SAR) and improving the CXCR2 antagonistic potency of this pyrido[3,4-]pyrimidine via systematic structural modifications of the substitution pattern. Almost all new analogues completely lacked the CXCR2 antagonism, the exception being a 6-furanyl-pyrido[3,4-]pyrimidine analogue (compound ) that is endowed with similar antagonistic potency as the original hit.
Topics: Humans; Neoplasms; Pyrimidines; Receptors, Chemokine; Structure-Activity Relationship; Receptors, Interleukin-8B
PubMed: 36903345
DOI: 10.3390/molecules28052099 -
Journal of Medicinal Chemistry Feb 2019The clinical evidence for the success of tyrosine kinase inhibitors in combination with microtubule-targeting agents prompted us to design and develop single agents that...
Design, Synthesis, and Biological Evaluation of 6-Substituted Thieno[3,2- d]pyrimidine Analogues as Dual Epidermal Growth Factor Receptor Kinase and Microtubule Inhibitors.
The clinical evidence for the success of tyrosine kinase inhibitors in combination with microtubule-targeting agents prompted us to design and develop single agents that possess both epidermal growth factor receptor (EGFR) kinase and tubulin polymerization inhibitory properties. A series of 6-aryl/heteroaryl-4-(3',4',5'-trimethoxyanilino)thieno[3,2- d]pyrimidine derivatives were discovered as novel dual tubulin polymerization and EGFR kinase inhibitors. The 4-(3',4',5'-trimethoxyanilino)-6-( p-tolyl)thieno[3,2- d]pyrimidine derivative 6g was the most potent compound of the series as an antiproliferative agent, with half-maximal inhibitory concentration (IC) values in the single- or double-digit nanomolar range. Compound 6g bound to tubulin in the colchicine site and inhibited tubulin assembly with an IC value of 0.71 μM, and 6g inhibited EGFR activity with an IC value of 30 nM. Our data suggested that the excellent in vitro and in vivo profile of 6g may be derived from its dual inhibition of tubulin polymerization and EGFR kinase.
Topics: Apoptosis; Cell Cycle; Cell Line, Tumor; Cell Proliferation; Colchicine; Drug Design; Drug Evaluation, Preclinical; Enzyme Activation; ErbB Receptors; HeLa Cells; Humans; Membrane Potential, Mitochondrial; Microtubules; Poly(ADP-ribose) Polymerases; Polymerization; Pyrimidines; Reactive Oxygen Species; Tubulin; Vascular Endothelial Growth Factor Receptor-2
PubMed: 30633509
DOI: 10.1021/acs.jmedchem.8b01391