Pyrimidine Series Research Articles

σ-Complexes in the Pyrimidine Series. 14. Dihydropyrimidine Analogs of Acyclonucleosides. Synthesis of 2,3-Dihydroxypropyl Derivatives of 4-Aryl-6-methyl-5-nitro-1,4(3,4)-dihydropyrimidin-2-ones

Methods have been developed for the synthesis of 5-nitro-1,4- and 5-nitro-3,4-dihydropyrimidin-2-one analogs of acyclonucleosides containing a 2,3-dihydroxypropyl fragment in positions 1 and 3 respectively of the dihydropyrimidine ring.

Synthesis and binding properties of oligo-2'-deoxyribonucleotides conjugated with triple-helix-specific intercalators: benzo[e] and benzo[g] pyridoindoles.

DNA binding compounds, such as benzo[e] (BePI) and benzo[g] pyridoindole (BgPI) derivatives, exhibit preferential stabilization of triple helices. We report here the synthesis of a series of pyrimidine triple-helix-forming oligo-2'-deoxyribonucleotides conjugated with these molecules. BePI was coupled to the 5-position of 2'-deoxyuridine via two linkers of different sizes attached to its 11-position and placed at either the 5'-end, inside the sequence, or at both the 5'-end and the internal positions using periodate oxidation of a diol-containing oligonucleotide followed by reductive coupling with amino-linked BePI. The same BePI derivatives were also linked to the oligonucleotide chain via internucleotidic phosphorothiolate or phosphoramidate linkages. A mixture of diastereoisomers was prepared as well as separate pure Rp and Sp isomers. A BePI derivative, with two different linkers attached to its 3-position, and BgPI derivatives were also linked to the 5-position of a 2'-deoxyuridine located at either the 5'-end or inside the sequence, as well as to the beta- anomeric position of an additional 2'- deoxyribose placed inside the sequence. The binding properties of these oligonucleotide-benzopyridoindoles conjugates with their double-stranded DNA target was studied by absorption spectroscopy.

Optimization of a pyrazolo[1,5- a]pyrimidine class of KDR kinase inhibitors: improvements in physical properties enhance cellular activity and pharmacokinetics

We have introduced solubilizing functionality to a 3,6-disubstituted pyrazolo[1,5- a]pyrimidine series of KDR kinase inhibitors to improve the physical properties of these compounds. The addition of a basic side-chain to the 6-aryl ring, introduction of 3-pyridyl groups, and most significantly, incorporation of a 4-pyridinonyl substituent at the 6-position of the core are modifications that maintain and often enhance the intrinsic potency of this class of inhibitors. Moreover, the improvements in physical properties result in marked increases in cellular activity and more favorable pharmacokinetics in rats. The synthesis and SAR of these compounds are described.

N-(Pyrimidin-4-yl) and N-(Pyridin-2-yl) phenylalanine derivatives as VLA-4 integrin antagonists

The SAR studies to optimise both potency and rate of clearance in the rat for a series of pyrimidine and pyridine based VLA-4 antagonists are described.

From Imidazoles to Pyrimidines: New Inhibitors of Cytokine Release

On the basis of model imidazole inhibitors of cytokine release, a series of novel pyridinyl pyrimidine derivatives was prepared and tested on their ability to inhibit the release of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) from peripheral blood mononuclear cells (PBMC) and human whole blood. In the pyrimidine series, structure-activity relationships (SARs) similar to those of the imidazole series were found, although generally pyrimidine compounds were less potent. Modification of the substituent at the 2 position of the pyrimidine led to the most active compound 14 which inhibited release of TNF-alpha (IC(50) = 3.2 microM) and IL-1beta (IC(50) = 2.3 microM) from PBMC as effectively as the model imidazole inhibitor ML 3163 (TNF-alpha, IC(50) = 3.7 microM; IL-1beta, IC(50) = 0.9 microM). Screening in an isolated enzyme assay revealed both imidazole and pyrimidine compounds as inhibitors of p38 MAP (mitogen-activated protein) kinase.

Cyclic Voltammetry as an Indicator of Antioxidant Activity

A series of compounds based around combining the neuroprotective properties of non-competitive N-methyl D-aspartic acid (NMDA) receptor antagonists with antioxidant functionalities have been prepared. The redox chemistry of these compounds has been evaluated using cyclic voltammetry, and the results have been compared with their radical-scavenging properties obtained from two standard biological assays, the inhibition of lipid peroxidation (thiobarbituric acid reacting substances assay) and the Sapphire colorimetric assay. Results from these different methods show general concordance. The most effective antioxidants were substituted phenols, e.g. Trolox�. The antioxidant activity of a series of pyrimidines was shown to be dependent on the presence of three amino substituents.

Cyclic Voltammetry as an Indicator of Antioxidant Activity

A series of compounds based around combining the neuroprotective properties of non-competitive N-methyl D-aspartic acid (NMDA) receptor antagonists with antioxidant functionalities have been prepared. The redox chemistry of these compounds has been evaluated using cyclic voltammetry, and the results have been compared with their radical-scavenging properties obtained from two standard biological assays, the inhibition of lipid peroxidation (thiobarbituric acid reacting substances assay) and the Sapphire colorimetric assay. Results from these different methods show general concordance. The most effective antioxidants were substituted phenols, e.g. Trolox�. The antioxidant activity of a series of pyrimidines was shown to be dependent on the presence of three amino substituents.

Mutation of Gln125 to Asn selectively abolishes the thymidylate kinase activity of herpes simplex virus type 1 thymidine kinase.

The broad substrate specificity of herpes simplex virus type 1 (HSV-1) thymidine kinase (TK) has provided the basis for selective antiherpetic therapy and, more recently, suicide gene therapy for the treatment of cancer. We have now constructed an HSV-1 TK mutant enzyme, in which an asparagine (N) residue is substituted for glutamine (Q) at position 125, and have evaluated the effect of this amino acid change on enzymatic activity. In marked contrast with wild-type HSV-1 TK, which displays both thymidine kinase and thymidylate kinase activities, the HSV-1 TK(Q125N) mutant was unable to phosphorylate pyrimidine nucleoside monophosphates but retained significant phosphorylation activity for thymidine and a series of antiherpetic pyrimidine and purine nucleoside analogs. The abrogation of HSV-1 TK-associated thymidylate kinase activity resulted in a 100-fold accumulation of the monophosphate form of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) in osteosarcoma cells transfected with the HSV-1 TK(Q125N) gene compared with osteosarcoma cells expressing wild-type HSV-1 TK. BVDU monophosphate accumulation gave rise to a much greater inhibition of cellular thymidylate synthase in HSV-1 TK(Q125N) gene-transfected cells than wild-type HSV-1 TK gene-transfected osteosarcoma tumor cells without significantly changing the cytostatic potency of BVDU for the HSV-1 TK gene-transfected tumor cells. Accordingly, the presence of the Q125N mutation in HSV-1 TK gene-transfected tumor cells was found to result in a multilog decrease in the cytostatic activity of those pyrimidine nucleoside analogs that in their monophosphate form do not have marked affinity for thymidylate synthase [i.e., 1-beta-D-arabinofuranosylthymine and (E)-5-(2-bromovinyl)-1-beta-D-arabinofuranosyluracil].

Hydrophobicity Parameter of Diazines IV: A New Hydrogen‐Accepting Parameter of Monosubstituted (Di)azines for the Relationship of Partition Coefficients in Different Solvent Systems

We recently proposed a new hydrogen‐accepting scale, SHA, for each member of the substituted (di)azine series on the basis of the heat of formation calculated under various dielectric environments by the COSMO method. In this paper, the SHA scale was used to examine relationships between log PCL (PCL: CHCl3/H2O partition coefficient) and log Poct (Poct: 1‐octanol/H2O partition coefficient) for each of the 2‐substituted pyridine (I), monosubstituted pyrazine (II), and pyrimidine (III) series. This SHA parameter worked nicely, representing the hydrogen‐accepting effect of the solute molecule. A correlation equation with excellent quality, such as log PCL = a log Poct + sSHA + constant, was obtained for each series. We further defined the parameter SHA/PY, derived from SHA values for the heterocyclic series by shifting the reference points to unsubstituted pyridine, to unify separately derived correlation equations. Thus, the correlation between log PCL and log Poct for all combined data of three series was derived by using a single equation as log PCL = a log Poct + sSHA/PY + constant. The SHA parameters were reasonably considered as being free‐energy related, and the rationale for the hydrogen‐bond‐acceptor scale was presented. © 2000 Wiley‐Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 89:1505–1517, 2000

Effect of Molecular Polarity and Conjugated System on Antiferroelectricity in AFLC's

Series of pyrimidine and pyridine analogous compounds have been developed in order to interpret the relationship between stability of antiferroelectricity and the conjugation along the long axis of the molecule. On the appearance of antiferroelectricity, the longitudinal polarization of whole molecules promotes to stabilize the antiferroelectricity.

Synthesis of acyclic nucleoside phosphonates as antiviral compounds

Reaction of 6-chloropyrimidines with diethyl [(2-aminoethoxy)methyl]phosphonate allows for a ready access to acyclic nucleoside phosphonates. A series of 5-substituted pyrimidines bearing a phosphonate side chain at position 6 were synthesized and tested against herpes simplex viruses (HSV-1 and HSV-2) and human immunodeficiency virus (HIV-1). Some compounds showed weak antiviral activity against HSV-1.

Synthesis and biological activities of 2′-deoxy-2′-fluoro-4′-thioarabinofuranosylpyrimidine and -purine nucleosides

As part of our ongoing investigation of the synthesis of biologically interesting 2′-modified-4′-thionucleosides, we synthesized 2′-deoxy-2′-fluoro-4′-thioarabinofuranosylpyrimidine and -purine nucleosides, and evaluated their antiviral and antitumor activities. In the pyrimidine series, β-anomers of 5-ethyluracil, 5-iodouracil, 5-chloroethyluracil, and 5-iodocytosine derivatives showed potent and selective anti-HSV-1 and HSV-2 activities in vitro. In the purine series, guanine and 2,6-diaminopurine derivatives showed prominent antiviral activities with slight cytotoxicity. On the other hand, the 5-fluorocytosine derivative (5F-4′-thioFAC) showed potent antitumor activity against both leukemia and solid tumor. Its antitumor spectrum against 14 human solid tumor and one leukemic cell lines was compared with that of 4′-thioFAC. The results showed that 5F-4′-thioFAC had an antitumor spectrum similar to that of 4′-thioFAC. However, 5F-4′-thioFAC was about 10 times less active than 4′-thioFAC.

Tyrosine kinase inhibitors. 17. Irreversible inhibitors of the epidermal growth factor receptor: 4-(phenylamino)quinazoline- and 4-(phenylamino)pyrido[3,2-d]pyrimidine-6-acrylamides bearing additional solubilizing functions.

4-Anilinoquinazoline- and 4-anilinopyrido[3,2-d]pyrimidine-6-acrylamides substituted with solubilizing 7-alkylamine or 7-alkoxyamine side chains were prepared by reaction of the corresponding 6-amines with acrylic acid or acrylic acid anhydrides. In the pyrido[3,2-d]pyrimidine series, the intermediate 6-amino-7-alkylamines were prepared from 7-bromo-6-fluoropyrido[3,2-d]pyrimidine via Stille coupling with the appropriate stannane under palladium(0) catalysis. This proved a versatile method for the introduction of cationic solubilizing side chains. The compounds were evaluated for their inhibition of phosphorylation of the isolated EGFR enzyme and for inhibition of EGF-stimulated autophosphorylation of EGFR in A431 cells and of heregulin-stimulated autophosphorylation of erbB2 in MDA-MB 453 cells. Quinazoline analogues with 7-alkoxyamine solubilizing groups were potent irreversible inhibitors of the isolated EGFR enzyme, with IC(50[app]) values from 2 to 4 nM, and potently inhibited both EGFR and erbB2 autophosphorylation in cells. 7-Alkylamino- and 7-alkoxyaminopyrido[3,2-d]pyrimidines were also irreversible inhibitors with equal or superior potency against the isolated enzyme but were less effective in the cellular autophosphorylation assays. Both quinazoline- and pyrido[3,2-d]pyrimidine-6-acrylamides bound at the ATP site alkylating cysteine 773, as shown by electrospray ionization mass spectrometry, and had similar rates of absorptive and secretory transport in Caco-2 cells. A comparison of two 7-propoxymorpholide analogues showed that the pyrido[3,2-d]pyrimidine-6-acrylamide had greater amide instability and higher acrylamide reactivity, being converted to glutathione adducts in cells more rapidly than the corresponding quinazoline. This difference may contribute to the observed lower cellular potency of the pyrido[3,2-d]pyrimidine-6-acrylamides. Selected compounds showed high in vivo activity against A431 xenografts on oral dosing, with the quinazolines being superior to the pyrido[3,2-d]pyrimidines. Overall, the quinazolines proved superior to previous analogues in terms of aqueous solubility, potency, and in vivo antitumor activity, and one example (CI 1033) has been selected for clinical evaluation.

ChemInform Abstract: Structure—Antiviral Activity Relationship in the Series of Pyrimidine and Purine N‐[2‐(2‐Phosphonomethoxy)ethyl] Nucleotide Analogues. Part 1. Derivatives Substituted at the Carbon Atoms of the Base.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase inhibitors and antitumor agents: synthesis and biological activities of 2,4-diamino-5-methyl-6-[(monosubstituted anilino)methyl] pyrido[2,3-d]pyrimidines.

Thirteen 2,4-diamino-5-methyl-6-[(monosubstituted anilino)methyl]pyrido[2,3-d]pyrimidines 5-17 were synthesized as potential Pneumocystis carinii (pc) and Toxoplasma gondii (tg) dihydrofolate reductase (DHFR) inhibitors and as antitumor agents. Compounds 5-17 were designed to investigate the structure-activity relationship of monomethoxy and monohalide substitution in the phenyl ring and N10-methylation of the C9-N10 bridge. The synthetic route to compounds 5-12 involved the reductive amination of a common intermediate, 2,4-diamino-5-methylpyrido[2, 3-d]pyrimidine-6-carbonitrile (18), with the appropriate anilines. N10-Methylation was achieved by reductive methylation. In contrast to previous reports of trimethoprim, the removal of methoxy and chloro groups from the phenyl ring in the 2, 4-diamino-5-methyl-6-[(substituted anilino)methyl]pyrido[2, 3-d]pyrimidine series generally did not decrease DHFR inhibitory activity. The monosubstituted phenyl analogues 5-12 were as potent against pcDHFR and tgDHFR as the previously reported disubstituted phenyl analogues. N10-Methylation generally resulted in a marginal increase in potency against both pcDHFR and tgDHFR. Compounds 5, 7, and 9 were evaluated and shown to inhibit the growth of T. gondii cells in culture at nanomolar concentrations. Compounds 6-8, 9, 11, and 16 were selected by the National Cancer Institute for evaluation in an in vitro preclinical antitumor screening program. All six compounds showed GI50 values in the 10(-7)-10(-9) M range in more than 20 cell lines.

Structure-antiviral activity relationship in the series of pyrimidine and purine N-[2-(2-phosphonomethoxy)ethyl] nucleotide analogues. 1. Derivatives substituted at the carbon atoms of the base.

A series of dialkyl esters of purine and pyrimidine N-[2-(phosphonomethoxy)ethyl] derivatives substituted at position 2, 6, or 8 of the purine base or position 2, 4, or 5 of the pyrimidine base were prepared by alkylation of the appropriate heterocyclic base with 2-chloroethoxymethylphosphonate diester in the presence of sodium hydride, cesium carbonate, or 1,8-diazabicyclo[5,4, 0]undec-7-ene (DBU) in dimethylformamide. Additional derivatives were obtained by the transformations of the bases in the suitably modified intermediates bearing reactive functions at the base moiety. The diesters were converted to the corresponding monoesters by sodium azide treatment, while the free acids were obtained from the diester by successive treatment with bromotrimethylsilane and hydrolysis. None of the PME derivatives in the pyrimidine series, their 6-aza or 3-deaza analogues, exhibited any activity against DNA viruses or retroviruses tested, except for the 5-bromocytosine derivative. Substitution of the adenine ring in PMEA at position 2 by Cl, F, or OH group decreased the activity against all DNA viruses tested. PMEDAP was highly active against HSV-1, HSV-2, and VZV in the concentration range (EC50) of 0.07-2 microg/mL. Also the 2-amino-6-chloropurine derivative was strongly active (EC50 = 0.1-0. 4 microg/mL) against herpes simplex viruses and (EC50 = 0.006-0.3 microg/mL) against CMV and VZV. PMEG was the most active compound of the whole series against DNA viruses (EC50 approximately 0.01-0.02 microg/mL), though it exhibited significant toxicity against the host cells. The base-modified compounds did not show any appreciable activity against DNA viruses except for 7-deazaPMEA (IC50 approximately 7.5 microg/mL) against HIV-1 and MSV. The neutral (diisopropyl, diisooctyl) diesters of PMEA were active against CMV and VZV, while the corresponding monoesters were inactive. The diisopropyl ester of the 2-chloroadenine analogue of PMEA showed substantially (10-100x) higher activity against CMV and VZV than the parent phosphonate. Also, the diisopropyl and diisooctyl ester of PMEDAP inhibited CMV and VZV, but esterification of the phosphonate residue did not improve the activity against either MSV or HIV.

ChemInform Abstract: σ‐Complexes in Pyrimidine Series. Part 13. Reaction of 7‐ and 5‐Methoxyfuroxano[3,4‐d]pyrimidines with Some C‐Nucleophiles.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

1-Cyclopentyluracils: Synthesis and conformational analysis by X-ray crystallography and AM1 theoretical calculations

A series of 1-cyclopentyl 5-substituted pyrimidines was synthesized and their energy-minimized structures were determined by AM1 and compared with the crystal structure of the parent compound, 1-cyclopentyluracil ( 2). As has been reported for other nucleoside analogues, the energy-minimized conformations were similar for all the compounds, but were not fully in agreement with the X-ray crystal structure obtained for 2.

Intramolecular cyclization of 2-(o-carboran-1-yl) methylthio-3-cyanopyridines in basic conditions

Substituted 2-(o-carboran-1-yl)methylthio-3-cyanopyridines and-pyrimidines undergo Thorpe-Ziegler cyclization under the influence of KOH in DMF to give the corresponding thienopyridines and thienopyrimidines. The reaction is complicated by a side reaction in which thecloso-carborane nucleus is converted to anido-system. The yield of thienopyridines containing acloso-carborane unit is increased by introduction of an acceptor substituent in the pyridine ring. Destruction of thecloso-carborane nucleus is not observed with the pyrimidine derivatives. The structures of the series of new carborane-containing thienopyridines and pyrimidines was confirmed by spectroscopic methods.

Reactions of potentially tautomeric methyl and methylene derivatives of pyridine and diazines with N-electrophiles (review)

Data on the nitration, nitrosation, azo-coupling, and electrophilic amination of potentially tautomeric methyl and methylene derivatives of a series of pyridines, pyridazines, pyrimidines, and pyrazines in media of varying acidity and basicity are reviewed systematically.