Uracil Ring Research Articles

Synthesis of 1‐(Alkyl)‐5‐dimethylamino‐6‐phenethyluracils as Potent Nonnucleoside HIV‐1 RT Inhibitors

1‐(Alkyl)‐5‐dimethylamino‐6‐phenethyl uracils (1) and (2) are analogs of MKC‐442, which is a very potent inhibitor of HIV‐1 reverse transcriptase. The target compound 1 was synthesized by the first approach, from the corresponding 1,3‐dibenzyl‐5‐(dimethylamino)‐6‐phenethylpyrimidine‐2,4(1H,3H)‐dione (7), which was synthesized in four steps from 6‐methyluracil (3) by nitration, benzylation, reduction, and methylation of the amino group. Compound 7 was then debenzylated to give the complete deprotected compound 8 with very low yield. To improve the yield, another pathway was developed for introducing the ethoxymethyl group at N‐1 of the uracil ring first. The result of adjusting reaction sequences increased the overall yield dramatically. All synthesized compounds were tested for their inhibition of HIV‐1 reverse transcriptase, and moderate activity was found for target compound 1.

Copper(II)–π interaction in cis-[Cu(orotato)(NH 3) 2] and the crystal structure of [Cu(orotato)(H 2O) 4] · H 2O: X-ray, vibrational spectroscopy and density functional study

The crystal structure of cis-[Cu(orotato)(NH 3) 2] ( 1) has been reinvestigated, and the structure of [Cu(orotato)(H 2O) 4] · H 2O ( 2) has been determined by single crystal X-ray diffraction and vibrational spectroscopic methods. In both complexes, the copper(II) ion is chelated by the deprotonated nitrogen atom (N1) of the uracil ring and the carboxylate oxygen atom of the orotate ligand. The square-planar environment of Cu is completed by two ammonia N atoms in 1, and two water O atoms in 2. Evidence is presented that the coordination sphere in 1 should be described as a (4+1+1)-geometry, where one axial position is occupied by the carbonyl oxygen atom and the other apical coordination site is located at the C C double bond of the neighboring uracilate ring. The non-covalent Cu(II)–π binding force is very important in stabilizing the columnar, polymeric structure of 1. The molecular structure of 2 is an asymmetric elongated octahedron (4+2) with two long Cu–O (water) axial bonds. Theoretical studies have been performed using the density functional unrestricted UB3LYP method. The natural charges on the atoms are derived from natural bond orbital (NBO) analysis. It is suggested that the π-type interaction between the chelated Cu 2+ cation and the aromatic compounds can play a significant role in biological systems, e.g. in the active sites of copper enzymes.

New Approach for the Synthesis of 1‐Aryl‐ and 1‐Heteroaryl‐5‐nitrouracil Derivatives.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Synthesis and Pharmacological Characterization of N3-Substituted Willardiine Derivatives: Role of the Substituent at the 5-Position of the Uracil Ring in the Development of Highly Potent and Selective GLUK5 Kainate Receptor Antagonists

Some N3-substituted analogues of willardiine such as 11 and 13 are selective kainate receptor antagonists. In an attempt to improve the potency and selectivity for kainate receptors, a range of analogues of 11 and 13 were synthesized with 5-substituents on the uracil ring. An X-ray crystal structure of the 5-methyl analogue of 13 bound to GLUK5 revealed that there was allowed volume around the 4- and 5-positions of the thiophene ring, and therefore the 4,5-dibromo and 5-phenyl (67) analogues were synthesized. Compound 67 (ACET) demonstrated low nanomolar antagonist potency on native and recombinant GLUK5-containing kainate receptors (KB values of 7 +/- 1 and 5 +/- 1 nM for antagonism of recombinant human GLUK5 and GLUK5/GLUK2, respectively) but displayed IC50 values >100 microM for antagonism of GLUA2, GLUK6, or GLUK6/GLUK2.

The molecular architecture of glucose‐1‐phosphate uridylyltransferase

Glucose-1-phosphate uridylyltransferase, also referred to as UDP-glucose pyrophosphorylase or UGPase, catalyzes the formation of UDP-glucose from glucose-1-phosphate and UTP. Not surprisingly, given the central role of UDP-glucose in glycogen synthesis and in the production of glycolipids, glycoproteins, and proteoglycans, the enzyme is ubiquitous in nature. Interestingly, however, the prokaryotic and eukaryotic forms of the enzyme are unrelated in amino acid sequence and structure. Here we describe the cloning and structural analysis to 1.9 A resolution of the UGPase from Escherichia coli. The protein is a tetramer with 222 point group symmetry. Each subunit of the tetramer is dominated by an eight-stranded mixed beta-sheet. There are two additional layers of beta-sheet (two and three strands) and 10 alpha-helices. The overall fold of the molecule is remarkably similar to that observed for glucose-1-phosphate thymidylyltransferase in complex with its product, dTDP-glucose. On the basis of this similarity, a UDP-glucose moiety has been positioned into the active site of UGPase. This protein/product model predicts that the side chains of Gln 109 and Asp 137, respectively, serve to anchor the uracil ring and the ribose of UDP-glucose to the protein. The beta-phosphoryl group of the product is predicted to lie within hydrogen bonding distance to the epsilon-nitrogen of Lys 202 whereas the carboxylate group of Glu 201 is predicted to bridge the 2'- and 3'-hydroxyl groups of the glucosyl moiety. Details concerning the overall structure of UGPase and a comparison with glucose-1-phosphate thymidylyltransferase are presented.

New approach for the synthesis of 1-aryl- and 1-heteroaryl-5-nitrouracil derivatives

1-(2,4-Dinitrophenyl)-5-nitrouracil and its 3-methyl derivatives were synthesized and used as substrates in reaction with aromatic amines and amino pyridines. In the reaction of aniline with 1-(2,4-dinitrophenyl)-5-nitrouracil, only the acyclic adduct was isolated. When 1-(2,4-dinitrophenyl)-3-methyl-5-nitrouracil was treated with aniline and other aromatic amines or amino pyridines, the desired 1-aryl-5-nitrouracil derivatives were obtained in satisfactory yield. The influence of the free H-3 proton present in the uracil ring on the course of the reaction is discussed.

6-Amino-1,3-dimethyl-5-(4-methylthiazol-2-yldiazenyl)uracil

In the mol­ecule of the title compound, C10H12N6O2S, the thia­zole ring is oriented with respect to the uracil ring at a dihedral angle of 8.08 (9)°. In the crystal structure, mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds, forming infinite chains running along the [001] direction.

Uracil ring opening in the reaction of 5-formyl-2′-deoxyuridine with primary alkyl amines

Treatment of 5-formyl-2′-deoxyuridine (f 5dU) with stoichiometric amounts of strongly nucleophilic, non-hindered primary alkyl amines led to fast and quantitative formation of the corresponding Schiff bases. In the presence of excess amines, novel nucleosides with ring opened pyrimidine bases were formed as a result of the Michael addition of a second amine to the pre-formed imines. In the reaction of f 5dU with aromatic amines, the formation of Schiff base derivatives was slower and even under prolonged treatment with an excess of amine the uracil ring remained intact.

A Convenient Method for N‐1 Arylation of Uracil Derivatives.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Structure-activity relationships of uridine 5'-diphosphate analogues at the human P2Y6 receptor.

The structure-activity relationships and molecular modeling of the uracil nucleotide activated P2Y6 receptor have been studied. Uridine 5'-diphosphate (UDP) analogues bearing substitutions of the ribose moiety, the uracil ring, and the diphosphate group were synthesized and assayed for activity at the human P2Y6 receptor. The uracil ring was modified at the 4 position, with the synthesis of 4-substituted-thiouridine 5'-diphosphate analogues, as well as at positions 2, 3, and 5. The effect of modifications at the level of the phosphate chain was studied by preparing a cyclic 3',5'-diphosphate analogue, a 3'-diphosphate analogue, and several dinucleotide diphosphates. 5-Iodo-UDP 32 (EC50 = 0.15 microM) was equipotent to UDP, while substitutions of the 2'-hydroxyl (amino, azido) greatly reduce potency. The 2- and 4-thio analogues, 20 and 21, respectively, were also relatively potent in comparison to UDP. However, most other modifications greatly reduced potency. Molecular modeling indicates that the beta-phosphate of 5'-UDP and analogues is essential for the establishment of electrostatic interactions with two of the three conserved cationic residues of the receptor. Among 4-thioether derivatives, a 4-ethylthio analogue 23 displayed an EC50 of 0.28 microM, indicative of favorable interactions predicted for a small 4-alkylthio moiety with the aromatic ring of Y33 in TM1. The activity of analogue 19 in which the ribose was substituted with a 2-oxabicyclohexane ring in a rigid (S)-conformation (P = 126 degrees , 1'-exo) was consistent with molecular modeling. These results provide a better understanding of molecular recognition at the P2Y6 receptor and will be helpful in designing selective and potent P2Y6 receptor ligands.

Theoretical investigation of the tautomerism of isoorotic acid in gaseous and aqueous phases

AbstractIn the present investigation, the tautomeric and conformational equilibrium of isoorotic acid have been studied using Møller–Plesset second‐order (MP2) and density functional theory (DFT) methods in the gas phase and aqueous solution (ε = 78.5) using the IPCM model. The relative energies of these tautomers have been calculated at the two levels of theory using 6‐311++G** basis set. Energetics and relative stabilities of the tautomers were compared and analyzed in both the gaseous and aqueous phases. The results indicate that the diketo tautomer (iso) is the most stable form in the gas phase and water. The carboxylic substitution in the uracil ring does not alter its relative stability order of the tautomers. The proton affinity of the oxygen atoms and the deprotonation enthalpy of the NH bonds of isoorotic acid have been compared with recent data of uracil. The relative stability of both syn‐ and anti‐conformations was investigated and the syn form was found to be more stable by 17.65 kcal/mol. It was determined in ab initio calculations that an electron can attach to isoorotic acid, forming a stable anion better than uracil. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

The Influence of Base on Regioselectivity of 5-Substituted Uracils Addition to Michael Acceptors

Michael type addition reaction of 5-substituted uracil derivatives to methyl acrylate and acrylonitrile has been studied. The regioselectivity of adducts has been observed due to the 5-substituent present in the uracil ring and the applied base. When triethylamine was used as a deprotonating agent, exclusively N-1 adducts were obtained. In the presence of DBU in DMF solution as the major products, N-3 adducts were isolated. Keywords: 5-substituted uracils, Michael addition, methyl acrylate, acrylonitrile

Synthesis of 6-[4-(allyl/phenyl)-5-thioxo-1,2,4-triazol-3-yl]pyrimidine-2,4-diones and their reaction with electrophiles

Cyclization of 1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-6-yl)carbonyl-4-R-thiosemicarbazides in basic medium gave 6-(4-R-5-thioxo-1,2,4-triazol-3-yl)pyrimidine-2,4-diones (R = Allyl, Ph). Alkylation of the latter with iodomethane occurred at the sulphur atom to give the corresponding methylsulfanyl derivatives. Acetylation using acetyl chloride occurred at the N(1) atom of the triazole ring to the corresponding acetyl derivative when R = Ph but for R = Allyl the acetylation did not occur under the same conditions. In the presence of bromine in refluxing methanol the indicated allyl-substituted compound cyclizes to 6-bromomethyl-3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-6-yl)-5,6-dihydrothiazolo[2,3-c]-1,2,4-triazole. Under Mannich and bromination conditions the methylsulfanyl derivatives prepared form derivatives at the 5 position of the uracil ring: 5-methylmorpholino-(piperidino)-and 5-bromo-(4-R-5-thioxo-1,2,4-triazol-3-yl)pyrimidine-2,4-diones respectively.

Structure−Activity Relationship Studies on N3-Substituted Willardiine Derivatives Acting as AMPA or Kainate Receptor Antagonists

N3-substitution of the uracil ring of willardiine with a variety of carboxyalkyl or carboxybenzyl substituents produces AMPA and kainate receptor antagonists. In an attempt to improve the potency and selectivity of these AMPA and kainate receptor antagonists a series of analogues with different terminal acidic groups and interacidic group spacers was synthesized and pharmacologically characterized. (S)-1-(2-Amino-2-carboxyethyl)-3-(2-carboxythiophene-3-ylmethyl)pyrimidine-2,4-dione (43, UBP304) demonstrated high potency and selectivity toward native GLU(K5)-containing kainate receptors (K(D) 0.105 +/- 0.007 microM vs kainate on native GLU(K5); K(D) 71.4 +/- 8.3 microM vs (S)-5-fluorowillardiine on native AMPA receptors). On recombinant human GLU(K5), GLU(K5)/GLU(K6), and GLU(K5)/GLU(K2), K(B) values of 0.12 +/- 0.03, 0.12 +/- 0.01, and 0.18 +/- 0.02 microM, respectively, were obtained for 43. However, 43 displayed no activity on homomeric GLU(K6) or GLU(K7) kainate receptors or homomeric GLU(A1-4) AMPA receptors (IC(50) values > 100 microM). Thus, 43 is a potent and selective GLU(K5) receptor antagonist.

Synthesis and Pharmacology of Willardiine Derivatives Acting as Antagonists of Kainate Receptors

The natural product willardiine (8) is an AMPA receptor agonist while 5-iodowillardiine (10) is a selective kainate receptor agonist. In an attempt to produce antagonists of kainate and AMPA receptors analogues of willardiine with substituents at the N3 position of the uracil ring were synthesized. The N3-4-carboxybenzyl substituted analogue (38c) was found to be equipotent at AMPA and GLUK5-containing kainate receptors in the neonatal rat spinal cord. The N3-2-carboxybenzyl substituted analogue (38a) proved to be a potent and selective GLUK5 subunit containing kainate receptor antagonist when tested on native rat and human recombinant AMPA and kainate receptor subtypes. The GLUK5 kainate receptor antagonist activity was found to reside in the S enantiomer (44a) whereas the R enantiomer (44b) was almost inactive. 5-Iodo substitution of the uracil ring of 44a gave 45, which was found to have enhanced potency and selectivity for GLUK5.

N‐Functionalization of Uracil Derivatives: Synthesis of Chiral 2‐(3‐Methyl‐5‐nitro‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)alkanoic Acids and Their Methyl Esters.

AbstractFor Abstract see ChemInform Abstract in Full Text.

An Efficient Alternative Route To 3,6-Disubstituted-Furo[2,3-d]Pyrimidin-2-One Analogues

Copper(I)-catalyzed 5-endo-dig cyclizations of 5-(alkyn-1-yl)uracil derivatives had given poor yields of substituted furo[2, 3]pyrimidin-2-ones unless the uracil ring was substituted at N1 with alkyl or glycosyl groups. This limited flexibility for the synthesis of analogues with varied substituents at N3 and/or C6 of the furo[2, 3]pyrimidin-2-one core has been overcome with 5-(3-hydroxyalkyn-1-yl)uracil compounds with no substituent at N1. Manipulation of the side-chain hydroxyl group gives access to additional furo[2,3-d]pyrimidin-2-one analogues.

Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it

Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)2, where NA denotes a nalidixic acid residue covalently linked to the 2′-position of 2′-amino-2′-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)2 of up to 53°C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)2. This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone–DNA complex in the active site of gyrases.

Structure of Escherichia coli UMP Kinase Differs from That ofOther Nucleoside Monophosphate Kinases and Sheds New Light on EnzymeRegulation

Structure of Escherichia coli UMP Kinase Differs from That ofOther Nucleoside Monophosphate Kinases and Sheds New Light on EnzymeRegulation

N-Functionalization of uracil derivatives: synthesis of chiral 2-(3-methyl-5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2 H)-yl)alkanoic acids and their methyl esters

3-Methyl-5-nitro-1-(4-nitrophenyl)uracil has been obtained by regioselective arylation of uracil using 4-nitrofluorobenzene, followed by methylation at the nitrogen atom N-3 and subsequent nitration of the uracil ring. 3-Methyl-5-nitro-1-(4-nitrophenyl)uracil, which was treated with either certain amino acids methyl ester or free amino acids underwent an ANRORC type substitution reaction. Appropriate methyl 2-substituted alkanoates or alkanoic acids containing 3-methyl-5-nitrouracil parts were obtained in satisfactory yields. A similar reaction can be carried out using 5-cyano-3-methyl-1-(4-nitrophenyl)uracil as a substrate.