A photoactive isoprenoid diphosphate analogue containing a stable phosphonate linkage: synthesis and biochemical studies with prenyltransferases

A number of biochemical processes rely on isoprenoids, including the post-translational modification of signaling proteins and the biosynthesis of a wide array of compounds. Photoactivatable analogues have been developed to study isoprenoid utilizing enzymes such as the isoprenoid synthases and prenyltransferases. While these initial analogues proved to be excellent structural analogues with good cross-linking capability, they lack the stability needed when the goals include isolation of cross-linked species, tryptic digestion, and subsequent peptide sequencing. Here, the synthesis of a benzophenone-based farnesyl diphosphate analogue containing a stable phosphonophosphate group is described. Inhibition kinetics, photolabeling experiments, as well as X-ray crystallographic analysis with a protein prenyltransferase are described, verifying this compound as a good isoprenoid mimetic. In addition, the utility of this new analogue was explored by using it to photoaffinity label crude protein extracts obtained from Hevea brasiliensis latex. Those experiments suggest that a small protein, rubber elongation factor, interacts directly with farnesyl diphosphate during rubber biosynthesis. These results indicate that this benzophenone-based isoprenoid analogue will be useful for identifying enzymes that utilize farnesyl diphosphate as a substrate.     

The iromycins, a new family of pyridone metabolites from Streptomyces sp. I. Structure, NOS inhibitory activity, and biosynthesis

The iromycins A-D are members of a new family of rare alpha-pyridone metabolites. The isolation and structure elucidation of these microbial secondary metabolites from Streptomyces sp. Dra 17 revealed a N-heterocyclic core structure with two unusual side chains. Iromycins act as inhibitors of nitric oxide synthases (NOS), a protein family, which produces the crucial second messenger nitric oxide (NO). Importantly, these compounds inhibit selectively endothelial NOS rather than neuronal NOS and thus set prospects for both medical therapy and basic research. Feeding experiments with 13C- and 15N -labeled precursors indicated an uncommon type of polyketide biosynthesis and clearly ruled out an isoprenoid origin. A detoxification pathway of a particular secondary metabolite in the host strain is a rare observation and here we demonstrate it with the iromycin family.     

Investigation into the formation of supramolecular compounds from mixed As/S-ligand complexes [(Cp*Mo)2As2S3] (Cp* = C5Me5) and copper halides

The coordination behavior of [(Cp*Mo)2As2S3] (3) (Cp* = C5Me5) toward Cu(I) halides was investigated. One dimensional polymers of the general formula [(Cp*Mo)2As2S3(CuHal)2]n (Hal = Cl, 4; Br, 5) and an oligomer of composition [{(Cp*Mo)2As2S3}3(CuI)7] (6) formed upon the reaction of 3 with the corresponding copper halide. All of the compounds were characterized by ESI-MS, elemental analysis, and single-crystal X-ray crystallography. The solid-state structures of 4 and 5 are isostructural and contain 1D S-shaped chains. This peculiar folding is achieved by alternating planar and folded Cu2Hal2 rings linked together by the central monosulfide bridge of the middle deck of the organometallic unit. The structure of 6 is characterized by a novel [CuI]7 aggregate, which forms a very flat Cu6I3S3 bowl along with three integrated peripheral [(Cp*Mo)2As2S3] building blocks. In contrast to earlier findings, the middle deck of the organometallic units consists in all structures of two trapezoidal AsS dumbbells and one monosulfide ligand.     

Influence of Brownian motion on blood platelet flow behavior and adhesive dynamics near a planar wall

We used the platelet adhesive dynamics computational method to study the influence of Brownian motion of a platelet on its flow characteristics near a surface in the creeping flow regime. Two important characterizations were done in this regard: (1) quantification of the platelet's ability to contact the surface by virtue of the Brownian forces and torques acting on it, and (2) determination of the relative importance of Brownian motion in promoting surface encounters in the presence of shear flow. We determined the Peclet number for a platelet undergoing Brownian motion in shear flow, which could be expressed as a simple linear function of height of the platelet centroid, H from the surface Pe (platelet) = . (1.56H + 0.66) for H > 0.3 microm. Our results demonstrate that at timescales relevant to shear flow in blood Brownian motion plays an insignificant role in influencing platelet motion or creating further opportunities for platelet-surface contact. The platelet Peclet number at shear rates >100 s-1 is large enough (>200) to neglect platelet Brownian motion in computational modeling of flow in arteries and arterioles for most practical purposes even at very close distances from the surface. We also conducted adhesive dynamics simulations to determine the effects of platelet Brownian motion on GPIbalpha-vWF-A1 single-bond dissociation dynamics. Brownian motion was found to have little effect on bond lifetime and caused minimal bond stressing as bond rupture forces were calculated to be less than 0.005 pN. We conclude from our results that, for the case of platelet-shaped cells, Brownian motion is not expected to play an important role in influencing flow characteristics, platelet-surface contact frequency, and dissociative binding phenomena under flow at physiological shear rates (>50 s(-1)).     

High-temperature rate constants for CH3OH + Kr --> products, OH + CH3OH --> products, OH + (CH3)(2)CO --> CH2COCH3 + H2O, and OH + CH3 --> CH) + H2O

The reflected shock tube technique with multipass absorption spectrometric detection of OH radicals at 308 nm (corresponding to a total path length of approximately 4.9 m) has been used to study the dissociation of methanol between 1591 and 2865 K. Rate constants for two product channels [CH3OH + Kr --> CH3 + OH + Kr (1) and CH3OH + Kr --> 1CH2 + H2O + Kr (2)] were determined. During the course of the study, it was necessary to determine several other rate constants that contributed to the profile fits. These include OH + CH3OH --> products, OH + (CH3)2CO --> CH2COCH3 + H2O, and OH + CH3 --> 1,3CH2 + H2O. The derived expressions, in units of cm(3) molecule(-1) s(-1), are k(1) = 9.33 x 10(-9) exp(-30857 K/T) for 1591-2287 K, k(2) = 3.27 x 10(-10) exp(-25946 K/T) for 1734-2287 K, kOH+CH3OH = 2.96 x 10-16T1.4434 exp(-57 K/T) for 210-1710 K, k(OH+(CH3)(2)CO) = (7.3 +/- 0.7) x 10(-12) for 1178-1299 K and k(OH+CH3) = (1.3 +/- 0.2) x 10(-11) for 1000-1200 K. With these values along with other well-established rate constants, a mechanism was used to obtain profile fits that agreed with experiment to within <+/-10%. The values obtained for reactions 1 and 2 are compared with earlier determinations and also with new theoretical calculations that are presented in the preceding article in this issue. These new calculations are in good agreement with the present data for both (1) and (2) and also for OH + CH3 --> products.     

Polynuclear lanthanide complexes of a series of bridging ligands containing two tridentate N,N',O-donor units: structures and luminescence properties

A set of three potentially bridging ligands containing two tridentate chelating N,N',O-donor (pyrazole-pyridine-amide) donors separated by an o, m, or p-phenylene spacer has been prepared and their coordination chemistry with lanthanide(III) ions investigated. Ligand L(1) (p-phenylene spacer) forms complexes with a 2:3 M:L ratio according to the proportions used in the reaction mixture; the Ln(2)(L(1))(3) complexes contain two 9-coordinate Ln(III) centres with all three bridging ligands spanning both metal ions, and have a cylindrical (non-helical) 'mesocate' architecture. The 1:1 complexes display a range of structural types depending on the conditions used, including a cyclic Ln(4)(L(1))(4) tetranuclear helicate, a Ln(2)(L(1))(2) dinuclear mesocate, and an infinite one-dimensional coordination polymer in which metal ions and bridging ligands alternate along the sequence. ESMS studies indicate that the 1:1 complexes form a mixture of oligonuclear species {Ln(L(1))}(n) in solution (n up to 5) which are likely to be cyclic helicates. In contrast, ligands L(2) and L(3) (with o- and m-phenylene spacers, respectively) generally form dinuclear Ln(2)L(2) Ln(III) complexes in which the two ligands may be arranged in a helical or non-helical architecture about the two metal ions. These complexes also contain an additional exogenous bidentate bridging ligand, either acetate or formate, which has arisen from hydrolysis of solvent molecules promoted by the Lewis-acidity of the Ln(III) ions. Luminescence studies on some of the Nd(III) complexes showed that excitation into ligand-centred pi-pi* transitions result in the characteristic near-infrared luminescence from Nd(III) at 1060 nm.     

51V NMR chemical shifts calculated from QM/MM models of vanadium chloroperoxidase

(51)V NMR chemical shifts calculated from QM/MM-optimized (QM=quantum mechanical; MM=molecular mechanical) models of vanadium-dependent chloroperoxidase (VCPO) are presented. An extensive number of protonation states for the vanadium cofactor (active site of the protein) and a number of probable positional isomers for each of the protonation states are considered. The size of the QM region is increased incrementally to observe the convergence behavior of the (51)V NMR chemical shifts. A total of 40 models are assessed by comparison to experimental solid-state (51)V NMR results recently reported in the literature. Isotropic chemical shifts are found to be a poor indicator of the protonation state; however, anisotropic chemical shifts and the nuclear quadrupole tensors appear to be sensitive to changes in the proton environment of the vanadium nuclei. This detailed investigation of the (51)V NMR chemical shifts computed from QM/MM models provides further evidence that the ground state is either a triply protonated (one axial water and one equatorial hydroxyl group) or a doubly protonated vanadate moiety in VCPO. Particular attention is given to the electrostatic and geometric effects of the protein environment. This is the first study to compute anisotropic NMR chemical shifts from QM/MM models of an active metalloprotein for direct comparison with solid-state MAS NMR data. This theoretical approach enhances the potential use of experimental solid-state NMR spectroscopy for the structural determination of metalloproteins.     

Sterically bulky tris(triazolyl)borate ligands as water-soluble analogues of tris(pyrazolyl)borate

The recently synthesized 3-tert-butyl-5-methyl-1,2,4-triazole reacted with KBH4 to give the new potassium tris(3-tert-butyl-5-methyl-1,2,4-triazolyl)borate K(Ttz(tBu,Me)) ligand. Ttz(tBu,Me) formed a four-coordinate (Ttz(tBu,Me))CoCl complex and five-coordinate (Ttz(tBu,Me))CoNO3 and (Ttz(tBu,Me))ZnOAc complexes. When these complexes were compared to their Tp(tBu,Me) analogues, it was found that Ttz(tBu,Me) resulted in negligible steric differences. K(Ttz(tBu,Me)) is more water-soluble than K(Tp(tBu,Me)), so bulky tris(triazolyl)borate ligands should lead to functional models for enzyme active sites in an aqueous environment and the creation of water-soluble analogues of Tp catalysts.     

DNA three-way junction with a dinuclear iron(II) supramolecular helicate at the center: a NMR structural study

A tetracationic supramolecular helicate, [Fe2L3]4+ (L = C25H20N4), with a triple-helical architecture is found to induce the formation of a three-way junction (3WJ) of deoxyribonucleotides with the helicate located in the center of the junction. NMR spectroscopic studies of the interaction between the M enantiomer of the helicate and two different oligonucleotides, [5'-d(TATGGTACCATA)]2 and [5'-d(CGTACG)]2, show that, in each case, the 2-fold symmetry of the helicate is lifted, while the 3-fold symmetry around the helicate axis is retained. The 1:3 helicate/DNA stoichiometry estimated from 1D NMR spectra supports a molecular model of a three-way junction composed of three strands. Three separate double-helical arms of the three-way junction are chemically identical giving rise to one set of proton resonances. The NOE contacts between the helicate and DNA unambiguously show that the helicate is fitted into the center of the three-way junction experiencing a hydrophobic 3-fold symmetric environment. Close stacking interactions between the ligand phenyl groups and the nucleotide bases are demonstrated through unusually large downfield shifts (1-2 ppm) of the phenyl protons. The unprecedented 3WJ arrangement observed in solution has also been found to exist in the crystal structure of the helicate adduct of [d(CGTACG)2] (Angew. Chem., Int. Ed. 2006, 45, 1227).     

Novel heterocycles. 7. Reaction of 2-chloronicotinonitrile with thioureas. Synthesis of the pyrido[2,3-d]pyrimido-[2,1-b][1,3]thiazine ring system

N,N'-Dimethylthiourea and 3,4,5,6-tetrahydro-2-pyrimidinethiol were allowed to react with 2-chloro-nicotinonitrile ( 1 ) and their products investigated by standard methods and by carbon-13 nmr. In both instances, displacement of the chlorine occurred by nitrogen not the sulfur of the thioureas. Secondary cyclizations occurred by attack of nitrogen on the nitrile to furnish 3a , and by sulfur on the nitrile to give 4b , a new ring system. Tricyclic 4b was hydrolyzed in dilute acid to give 5 , or alkylated with methyl iodide in the presence of sodium hydride to give the ring opened product 6 .