Synthesis of 2′-Deoxy-5-(isothiazol-5-yl)uridine and Its Interaction with the HSV-1 Thymidine Kinase

2′-Deoxy-5-(isothiazol-5-yl)uridine ( 12 ) was synthesized starting from 2′-deoxy-5-iodouridine using a Pd-catalysed cross-coupling reaction with propiolaldehyde diethyl acetal followed by deprotection and ring closure using thiosulfate. 2′-Deoxyuridine 12 has a particular place among the 5-heteroaryl-substituted 2′-deoxyuridines in that it has a high affinity for herpes simplex virus type 1 (HSV-1)-encoded thymidine kinase (TK) without antiviral activity. Biochemical studies revealed that 12 is a substrate for viral TK. We further investigated the interaction of 12 with the HSV-1 thymidine kinase. The conformation of 12 in solution was established by NMR spectroscopy. The most stable conformer 12A has the S-atom of the isothiazole ring placed in the neighbourhood of the C(4)?O group of the pyrimidine moiety. The compound was docked in its most stable conformation in the active site of HSV-1 TK and subjected to energy minimization. This demonstrated that the isothiazole moiety binds in a cavity lined by the side chains of Tyr-132, Arg-163, Ala-167, and Ala-168 and that the C(3) atom of the isothiazole moiety is located in close proximity of the phenolic O-atom of Tyr-132 and the aliphatic part of the Arg-163 side chain.     

Tetrakis(diethyl‐phosphonat)‐, Tetrakis(ethyl‐phenylphosphinat)‐ und Tetrakis(diphenylphosphin‐oxid)‐substituierte Phthalocyanine

Tetrakis(diethyl phosphonate), Tetrakis(ethyl phenylphosphinate)‐, and Tetrakis(diphenylphosphine oxide)‐Substituted Phthalocyanines The title compounds 7, 9 , and 11 are obtained by tetramerization of diethyl (3,4‐dicyanophenyl)phosphonate ( 5 ), ethyl (3,4‐dicyanophenyl)phenylphosphinate ( 8 ), and 4‐(diphenylphosphinyl)benzene‐1,2‐dicarbonitrile ( 10 ). The ³¹P‐NMR spectra of the phthalocyanines 7, 9 , and 11 and of their metal complexes present five to eight signals confirming the formation of four constitutional isomers with the expected C_4h, D_2h, C_2v, and C_s symmetry. In the FAB‐MS of the Zn, Cu, and Ni complexes of 7 and 9 , the peaks of dimeric phthalocyanines are observed. By gel‐permeation chromatography, the monomeric complex [Ni( 7 )] and a dimer [Ni( 7 )]₂ can be separated. These dimers differ from the known phthalocyanine dimers, i.e., possibly the P(O)(OEt)₂ and P(O)(Ph)(OEt) substituents in 7 and 9 are involved in complexation. The free phosphonic acid complex [Zn( 12 )] and [Cu( 12 )] are H₂O‐soluble. In the FAB‐MS of [Zn( 12 )], only the peaks of the dimer are present; the ESI‐MS confirms the existence of the dimer and the metal‐free dimer. In the UV/VIS spectrum of [Zn( 12 )], the hypsochromic shift characteristic for the known type of dimers from 660–700 nm to 620–640 nm is observed. As in the FAB‐MS of [Zn( 12 )], the free phosphinic acid complex [Zn( 13 )] shows only the monomer, an ESI‐MS cannot be obtained for solubility problems. The UV/VIS spectrum of [Zn( 13 )] demonstrates the existence of the monomer as well as of the dimer.     

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A(3) forms a noncanonical base pair with A(8) in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.     

Dioxygen activation by a low-valent cobalt complex employing a flexible tripodal N-heterocyclic carbene ligand

The novel versatile cobalt(I) tris-carbene complex [(TIMEN(xyl))Co]Cl (1) (where TIMEN = (tris[2-(3-arylimidazol-2-ylidene)ethyl]amine) reacts with CO, one-electron oxidizers such as CH(2)Cl(2), and O(2) to yield the cobalt complexes [(TIMEN(xyl))Co(CO)]Cl (2), [(TIMEN(xyl))Co(Cl)]Cl (3), and peroxo species [(TIMEN(xyl))Co(O(2))](BPh(4)) (5). All new complexes were fully characterized by (1)H NMR, UV/vis, and IR spectroscopy as well as superconducting quantum interference device (SQUID) magnetization measurements and single-crystal X-ray crystallography. The nucleophilic character of the eta(2)-bound dioxygen ligand in 5 was confirmed by density functional theory (DFT) studies and allows for oxygen-transfer reactions with electron-deficient organic substrates, such as benzoyl chloride.     

Microcolumns with self-assembled particle frits for proteomics

LC-MS-MS experiments in proteomics are usually performed with packed microcolumns employing frits or outlets smaller than the particle diameter to retain the packing material. We have developed packed microcolumns using self-assembled particles (SAPs) as frits that are smaller than the size of the outlet. A five to one ratio of outlet size to particle diameter appears to be the upper maximum. In these situations the particles assembled into an arch over the outlet like the stones in a stone bridge. When 3 microm particles were packed into a tapered column with an 8 microm outlet, two particles bridged the outlet with 0.3 pl dead volume and perfect success rate. In peptide analysis by LC-MS, the peak width at half height was normally less than 6 s, compared to 12 s without SAPs. The LC-MS-MS system provided 37% sequence coverage (21 matched peptides) for a tryptically-digested sample of 10 fmol bovine serum albumin. We also describe application of the SAP principle to make disposable pipette tip columns with short pieces of fused-silica capillary as the outlet.     

Conformational energies and rotational barriers in 3-methyl-1-butene and 1-butene: An ab initio and molecular mechanics study

The calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3-methyl-1-butene is not in agreement with experimental data. In order to reparametrize the C_sp2-C_sp3-C_sp-C_sp3 torsional angle, 3-methyl-1-butene and 1-butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6-31G* and MP3/6-31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3-methyl-1-butene and 1-butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.     

Liquid chromatographic analysis of vitamin B6 in reconstituted infant formula: collaborative study

A liquid chromatographic (LC) method was validated for the determination of total vitamin B6 in infant formula. Total vitamin B6 was quantified by converting the phosphorylated and free vitamers into pyridoxine. Pyridoxine was determined by ion pair reversed-phase LC with fluorescence detection. The method was subjected to an AOAC collaborative study involving a factory-manufactured, milk- and soy-based infant formula. Each was spiked at 3 concentrations in the range of 0-1 microg/g and sent as blind duplicate to participant laboratories. Nine laboratories returned valid data which were statistically analyzed for outliers and precision parameters. The repeatability relative standard deviation (RSD(r)) ranges were 2.0-4.0 and 3.5-5.9% for fortified milk- and soy-based formulas, respectively. The reproducibility relative standard deviation (RSD(R)) ranges were 8.2-8.4 and 6.7-11.2% for fortified milk- and soy-based formulas, respectively. HORRAT values ranged from 0.42 to 0.53, indicating that the precision of the method is acceptable. The mean RSD(r):RSD(R) values were 0.60 and 0.55 for milk- and soy-based formulas, respectively. As expected, RSDs for the unfortified samples were higher, but their HORRAT values (0.81 and 2.06) helped define a realistic limit of quantitation as 0.05 microg/g. Recovery data were quantitative and varied between 81.4 and 98.0% (mean = 89.8%) for each of 6 spiked materials.