Regeneration of the antiviral drug (E)-5-(2-bromovinyl)-2''-deoxyuridine in vivo

The highly potent and selective antiherpes drug BVdUrd [(E)-5-(2-bromovinyl)-2'-deoxyuridine] is cleared within 2-3 hours from the bloodstream upon intraperitoneal administration to rats. It is degraded to BVUra [(E)-5-(2-bromovinyl)uracil] and this inactive metabolite is cleared very slowly from the bloodstream so that 24 hours after the administration of BVdUrd, BVUra is still detectable in the plasma. This contrasts with several other 5-substituted uracils, i.e. 5-fluorouracil, 5-iodouracil, 5-trifluorothymine and thymine itself, which are, like their 2'-deoxyuridine counterparts FdUrd, IdUrd, F3dThd and dThd, cleared from the plasma within 2-3 hours. The injection of dThd or any of the other 5-substituted 2'-deoxyuridines at 3 hours after the injection of BVdUrd, that is at a time when BVdUrd has disappeared completely from the circulation, results in the re-apparition of BVdUrd in the plasma. Apparently, BVdUrd is regenerated from BVUra following the reaction catalyzed by pyrimidine nucleoside phosphorylases : BVUra + dThd----BVdUrd + Thy. BVdUrd can even be generated de novo if dThd (or FdUrd, IdUrd or F3dThd) are administered 3 hours after a preceding injection of BVUra. These findings represent a unique example of the (re)generation of an active drug from its inactive metabolite in vivo.     

Antiviral activity of the 3''-amino derivative of (E)-5-(2-bromovinyl)-2''-deoxyuridine.

3'-NH2-BV-dUrd, the 3'-amino derivative of (E)-5-(2-bromovinyl)-2'-deoxyuridine, was found to be a potent and selective inhibitor of herpes simplex virus type 1 (HSV-1) and varicella-zoster virus (VZV) replication. 3'-NH2-BV-dUrd was about 4-12 times less potent but equally selective in its anti-herpes activity as BV-dUrd. Akin to BV-dUrd, 3'-NH2-BV-dUrd was much less inhibitory to herpes simplex virus type 2 than type 1. It was totally inactive against a thymidine kinase-deficient mutant of HSV-1. The 5'-triphosphate of 3'-NH2-BV-dUrd (3'-NH2-BV-dUTP) was evaluated for its inhibitory effects on purified herpes viral and cellular DNA polymerases. Among the DNA polymerases tested, HSV-1 DNA polymerase and DNA polymerase alpha were the most sensitive to inhibition by 3'-NH2-BV-dUTP (Ki values 0.13 and 0.10 microM, respectively). The Km/Ki ratio for DNA polymerase alpha was 47, as compared with 4.6 for HSV-1 DNA polymerase. Thus, the selectivity of 3'-NH2-BV-dUrd as an anti-herpes agent cannot be ascribed to a discriminative effect of its 5'-triphosphate at the DNA polymerase level. This selectivity most probably resides at the thymidine kinase level. 3'-NH2-BV-dUrd would be phosphorylated preferentially by the HSV-1-induced thymidine kinase (Ki 1.9 microM, as compared with greater than 200 microM for the cellular thymidine kinase), and this preferential phosphorylation would confine the further action of the compound to the virus-infected cell.     

Modified polynucleotides. VI. Properties of a synthetic DNA containing the anti-herpes agent (E)-5-(2-bromovinyl)-2''-deoxyuridine

A new modified polydeoxynucleotide, a copolymer of nucleotides of 2'-deoxyadenosine and the very efficacious anti-herpesvirus agent (E)-5-(2-bromovinyl)-2'-deoxyuridine was synthesized with E. coli DNA polymerase I enzyme. It is characterized by its physical (absorption and circular dichroism spectra, thermal transition, sedimentation analysis) and bioorganic (template activity, stability) properties. Compared to poly [d(A-T)], the modified polydeoxynucleotide had a lower thermal stability but exhibited higher stability against DNases and higher template activity for DNA synthesis. Template activity for RNA synthesis of this template was, however, poor and extent of AMP and UMP incorporation was limited as well.     

Potent inhibitory effects of the 5'-triphosphates of (E)-5-(2-bromovinyl)-2'-deoxyuridine and (E)-5-(2-bromovinyl)-1-beta-D-arabinofuranosyluracil on DNA polymerase gamma

(E)-5-(2-Bromovinyl)-2'-deoxyuridine 5'-triphosphate (BrVdUTP) and (E)-5-(2-bromovinyl)-1-beta-D-arabinofuranosyluracil 5'-triphosphate (BrVarafUTP), which are known as specific inhibitors of herpes simplex viral (type 1 and 2) DNA polymerase, were found to be strong inhibitors of DNA polymerase gamma from human KB and murine myeloma cells. In fact BrVdUTP and BrVarafUTP were found to be stronger inhibitors of DNA polymerase gamma than of other DNA polymerases having viral (herpes simplex virus or retrovirus) origin or cellular (eukaryotic alpha and beta, or prokaryotic) origin. The mode of inhibition of DNA polymerase gamma by BrVdUTP and BrVarafUTP was competitive with respect to dTTP, the normal substrate. Whereas BrVdUTP was an efficient substrate for DNA polymerase gamma and other DNA polymerases that were examined, BrVarafUTP failed to serve as a substrate for DNA synthesis. Ki values for BrVdUTP (40 nM) and BrVarafUTP (7 nM) with DNA polymerase gamma, as determined with (rA)n.(dT) as the template.primer, were much smaller than the Km values for dTTP (0.16 microM and 0.71 microM for murine and human DNA polymerase gamma, respectively). Thus, the affinity of BrVdUTP or BrVarafUTP for DNA polymerase gamma was much stronger than that of dTTP.     

Inhibition of terminal deoxynucleotidyltransferase by (E)-5-(2-bromovinyl)-2'-deoxyuridine 5'-triphosphate

(E)-5-(2-bromovinyl)-2'-deoxyuridine 5'-triphosphate (BVdUTP), known as a specific inhibitor of herpes simplex virus (type 1)-DNA polymerase, was found to be a potent inhibitor of the activity of terminal deoxynucleotidyltransferase (TdT) from calf thymus. BVdUTP was not an efficient substrate of TdT, but it inhibited the incorporation of normal deoxynucleotide substrates in competitive fashion at the nucleotide binding site of TdT molecule. The Ki value for BVdUTP (5 microM) was much less than the Km value for dGTP (83 microM), indicating stronger affinity of the inhibitor to TdT than that of the substrate. These results indicate the usefulness of BVdUTP as a potent inhibitor of TdT for elucidation of the reaction mechanism of this enzyme.     

Crystal and molecular structure of methyl O-alpha-D-manno-pyranosyl-(1----2)-alpha-D-mannopyranoside

The crystal and molecular structure of a synthetic mannosyl disaccharide, methyl O-alpha-D-mannopyranosyl-(1----2)-alpha-D-mannopyranoside, has been determined from X-ray diffractometer data by direct methods by use of the Multan programs. The crystals are monoclinic, space group P2 with unit cell dimensions, a 8.086(1), b 9.775(1), c 9.975(2) A, beta 104.58(1) degrees, Z 2, and Dm 1.54 g/cm3. The structure was refined to an R-value of 0.033 for 1359 reflections measured with CuK alpha radiation. The mannopyranose units have the chair conformations 4C(D) with C-5' and C-2' deviating from the best plane through the other four atoms of the ring by -0.68 and +0.53 A in the nonreducing group, and C-3 and O-5 deviating from the mean plane through the other four atoms by +0.57 and -0.66 A, respectively, in the "potentially" reducing residue. The ring-to-ring conformation can be described as (phi, psi) = (-64.5, 105.5 degrees). The conformation across the C-5--C-6 bond is gauche-gauche in both the sugars. The crystal structure is stabilized by a network of intermolecular O-H...O hydrogen bonds.     

Crystal and molecular structure of [Cu(5'-inosine monophosphate) (dipyridylamine) (H2O)]2.4H2O.

The ternary complex [Cu(5′-IMP)(dpa)(H₂O)]₂ has been prepared and its structure analyzed by x-ray diffraction. It has a dimeric structure in which the 5′-IMP ligands coordinate solely through their phosphate groups. This geometry is in marked contrast to that of another $\text{Cu}\text{5′-}\text{IMP}$ ternary complex, [Cu(5′-IMPH)(bipy)(H₂O)₂]⁺, which shows metal binding through the purine base rather than the phosphate group.     

Enantiospecific synthesis of carbocyclic (+)-(E)-5-(2-bromovinyl)-2'-deoxyuridine

(+)-1-[(1R, 3S, 4R)-3-hydroxy-4-hydroxymethylcyclopentyl]-5-[(E)-2- bromovinyl]-1H,3H-pyrimidin-2,4-dione 10 was synthesized starting from (+)-endo-5-norbornen-2-yl acetate. This chiral educt was obtained by enzymatic hydrolysis of racemic esters of endo-5-norbornen-2-ol.     

(E)-5-(2-bromovinyl)-2'-deoxyuridine-5'-triphosphate as a DNA polymerase substrate.

Time course of incorporation and the effect of 5'-triphosphate of the selective antiherpetic agent (E)-5-(2-bromovinyl)-2'-deoxyuridine (bv5dUTP) on the incorporation of dTTP and dATP into template-primers of different structure were studied in E. coli DNA polymerase I Klenow fragment enzyme-catalyzed reactions. bv5dUTP could substitute for dTTP depending on the structure of template-primer. E.g. into calf thymus DNA incorporation of bv5dUMP was around 80% of that of dTMP at 30 minutes of incubation. The analog has also inhibited dTMP incorporation, net DNA synthesis, however, was hardly affected. The substrate properties of the analog were studied with [2-14C]-labelled bv5dUTP.     

Conformation of acetylcholine at muscarinic nerve receptors: Crystal and molecular structure of 2-trimethylammoniummethyl-5-methyl furan iodide (5-methylfurmethide iodide)

2-Trimethylammoniummethyl-5-methyl furan (5-methylfurmethide) is a potent cholinergic agonist at muscarinic nerve receptors. The conformation of the molecule, as shown by crystal structure analysis, is restricted by steric hindrance. The only similar conformation of acetylcholine has τ(N⁺CCO) synclinal and τ(CCOC) antiplanar. This is the conformation found in solution and in crystals of the chloride, and it is believed to be the one relevant to interaction with muscarinic nerve receptors.     

Crystal structure and conformation of 8-(2-hydroxyethylamino) and 8-(pyrrolidin-1-yl) adenosines

In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 2(1); a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) A, beta = 92.261(1) degrees, V = 707.10(3) A3, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2')-endo conformation and gauche-gauche form across C(4')-C(5') bond. The molecular structure is stabilized by intramolecular hydrogen bond of N-HO type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) A, beta = 103.254(2), V = 1524.4(2) degrees A3, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2')-endo conformation and gauche -gauche form across C(4')- C(5') bond. The molecular structure is stabilized by intramolecular hydrogen bond of O-HN type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.     

Crystal structure and possible catalytic mechanism of microsomal prostaglandin E synthase type 2 (mPGES-2)

Prostaglandin (PG) H(2) (PGH(2)), formed from arachidonic acid, is an unstable intermediate and is converted efficiently into more stable arachidonate metabolites (PGD(2), PGE(2), and PGF(2)) by the action of three groups of enzymes. Prostaglandin E synthase catalyzes an isomerization reaction, PGH(2) to PGE(2). Microsomal prostaglandin E synthase type-2 (mPGES-2) has been crystallized with an anti-inflammatory drug indomethacin (IMN), and the complex structure has been determined at 2.6A resolution. mPGES-2 forms a dimer and is attached to lipid membrane by anchoring the N-terminal section. Two hydrophobic pockets connected to form a V shape are located in the bottom of a large cavity. IMN binds deeply in the cavity by placing the OMe-indole and chlorophenyl moieties into the V-shaped pockets, respectively, and the carboxyl group interacts with S(gamma) of C110 by forming a H-bond. A characteristic H-bond chain formation (N-H...S(gamma)-H...S(gamma)...H-N) is seen through Y107-C113-C110-F112, which apparently decreases the pK(a) of S(gamma) of C110. The geometry suggests that the S(gamma) of C110 is most likely the catalytic site of mPGES-2. A search of the RCSB Protein Data Bank suggests that IMN can fit into the PGH(2) binding site in various proteins. On the basis of the crystal structure and mutation data, a PGH(2)-bound model structure was built. PGH(2) fits well into the IMN binding site by placing the alpha and omega-chains in the V-shaped pockets, and the endoperoxide moiety interacts with S(gamma) of C110. A possible catalytic mechanism is proposed on the basis of the crystal and model structures, and an alternative catalytic mechanism is described. The fold of mPGES-2 is quite similar to those of GSH-dependent hematopoietic prostaglandin D synthase, except for the two large loop sections.     

Incorporation of the carbocyclic analogue of (E)-5-(2-bromovinyl)-2'-deoxyuridine 5'-triphosphate into a synthetic DNA

The carbocyclic analogue of (E)-5-(2-bromovinyl)-2'-deoxyuridine, C-BVDU, is a very potent and selective anti-herpes-virus compound. In order to synthesize and study the properties of a DNA that contains C-BVDU, the 5'-triphosphate, C-BVDUTP was prepared and evaluated as a potential substrate of the E. coli Klenow DNA polymerase enzyme. Although C-BVDUTP proved to be a very poor substrate also of this enzyme, it could be incorporated up to 3.6% into the synthetic DNA, poly(dA-dT, C-BVDU). This level of substitution decreased significantly the template activity for DNA and RNA polymerases, as compared to that of poly(dA-dT).     

Synthesis and Biological Properties of (+) and (-)-(E)-5-(2-bronovinyl)-21 -deoxy-11 a-Carbauridine

Abstract

Carbocyclic (+)- and (-)-(E)-5- (2-bromovinyl)-2′-deoxyuridlne have been prepared from (+)- and (-)-endo-norborn-5-en-2-y1 butyrate. In cell cultures both (+)- and (-)-C-BVDU showed activity against herpes simplex virus types 1 and 2, (+)-C-BVDU being only slightly less active than BVDU itself. (-)-C-BVDU gave a smaller but still significant antiviral effect. A nomenclature for carbocyclic nucleosides is proposed.     

Copper(II) halide complexes of 2-aminobenzophenone. Crystal and molecular structure of bis(2-aminobenzophenone)dichlorocopper(II)

The complexes CuX₂L₂ (X = Cl, Br; L = 2-aminobenzophenone) were prepared and characterized by means of magnetic and spectroscopic measurements. For the Cl compound the crystal structure was also determined. Crystals are triclinic, space group P$\text{1}$, with a = 13.397(3), b = 10.752(2), c = 9.205(2) Å, α = 72.26(1)°, β = 91.58(1)°, γ = 106.86(1)°, and Z = 2. The structure was solved by the heavy-atom method and refined by least-squares calculations to R = 0.034 for 2581 counter data. It consists of discrete CuX₂L₂ monomers showing distorted trigonal bipyramidal coordination geometry about the copper ion. The amino nitrogens are axial ligands, with the equatorial positions occupied by two chlorine atoms and a carbonyl oxygen from one L molecule acting as a bidentate ligand. Infrared and ligand field spectroscopies and magnetic measurements, interpreted on the basis of the known crystal structure, also suggest a similar structure for the related Br compound.     

Crystal and molecular structure of a collagen-like polypeptide (Pro-Pro-Gly)10

(Pro-Pro-Gly)₁₀ forms single crystals, providing X-ray diffraction data to 0.22 nm resolution. In the crystals, the polypeptides form triplexes that aggregate end-to-end in quasi-infinite helices with axial translation per tripeptide h = 0.287 nm and the corresponding rotation t = ?102.9 °. The structure, which may be an allomorph of collagen, has been refined by the linked-atom least-squares procedure. In addition, three water molecules per tripeptide have been detected by Fourier difference syntheses. One of them forms an intrachain hydrogen-bonded bridge O(Pro₂) - - - W - - - O(Gly). There are also interchain hydrogen bonds (Gly)NH - - - O(Pro₁) within the triplex.     

Experimental and theoretical investigation of the molecular and electronic structure of 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine

The title molecule, 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine (C₂₀H₂₁N₃S), was prepared and characterized by ¹H-NMR, ¹³C-NMR, IR and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?9.4350(5) Å, b?=?11.2796(6) Å, c?=?18.4170(8) Å and β?=?113.378(3)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H- and ¹³C-NMR chemical shift values and atomic charges distribution of the title compound in the ground state have been calculated using the Hartree–Fock (HF) and density functional method (DFT) (B3LYP) with 6-31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis was performed by the B3LYP/6-31G(d) method.     

(E)-2-(2-Hydroxyethylidene)-6-methyl-5-heptenal (alpha-acariolal) and (E)-2-(2-hydroxyethyl)-6-methyl-2,5-heptadienal (beta-acariolal), two new types of isomeric monoterpenes from Caloglyphus polyphyllae (Acari: Acaridae)

The opisthonotal gland secretion of the acarid mite, Caloglyphus polyphyllae, contained two new monoterpenes, (E)-2-(2-hydroxyethylidene)-6-methyl-5-heptenal (1) and (E)-2-(2-hydroxyethyl)-6-methyl-2,5-heptadienal (2), to which we have given the trivial names alpha- and beta-acariolal in relation to alpha- and beta-acaridial (3 and 4), respectively. Elucidation of the structure of 1 was established mainly from 1H-NMR and GC/MS spectral data after partial purification, together with the fact that 1 was recovered in the more-polar fraction from a silica gel column than alpha- and beta-acaridial (3 and 4) present in the secretion. Compound 2 was obtained in the same fraction as a mixture with 1. Based on the facts that 2 had the same molecular weight by GC/MS and the same polarity as that of 1, compound 2 was assumed to be a structural analog of 1. The structures of compounds 1 and 2 were confirmed by their synthesis in nine and ten respective steps starting from alpha-bromo-gamma-butyrolactone.