Improved RNA cleavage by LNAzyme derivatives of DNAzymes.

Specific cleavage of RNA is catalysed by short oligodeoxynucleotides termed DNAzymes. DNAzymes consist of two binding arms that hybridize to a predetermined RNA sequence and a catalytic core that cleaves a phosphodiester bond held between the binding arms. DNAzymes are exemplified by the well-studied 10-23 DNAzyme, which compared with protein ribonucleases is highly specific, albeit slow. Here we report a significant improvement in cleavage kinetics, while maintaining specificity, by incorporation of LNA (locked nucleic acid) and alpha-L-LNA nucleotides into the binding arms of 10-23 DNAzyme. DNAzymes modified in this way (LNAzymes) enhance cleavage of a phosphodiester bond presented in a short RNA substrate as well as in longer and highly structured substrates, and efficient cleavage is maintained from single- to multiple-turnover conditions. Analysis of the cleavage reaction indicates that substrate hybridization is boosted by the presence of the locked residues within the LNAzymes, while no apparent change occurs in the catalytic strand-scission step.

Implications for isoform-selective inhibitor design derived from the binding mode of bulky isothioureas to the heme domain of endothelial nitric-oxide synthase.

Nitric oxide produced by nitric-oxide synthase (NOS) is not only involved in a wide range of physiological functions but also in a variety of pathological conditions. Isoform-selective NOS inhibitors are highly desirable to regulate the NO production of one isoform beneficial to normal physiological functions from the uncontrolled NO production of another isoform that accompanies certain pathological states. Crystal structures of the heme domain of the three NOS isoforms have revealed a very high degree of similarity in the immediate vicinity of the heme active site illustrating the challenge of isoform-selective inhibitor design. Isothioureas are potent NOS inhibitors, and the structures of the endothelial NOS heme domain complexed with isothioureas bearing small S-alkyl substituents have been determined (Li, H., Raman, C.S., Martásek, P., Král, V., Masters, B.S.S., and Poulos, T.L. (2000) J. Inorg. Biochem. 81, 133--139). In the present communication, the binding mode of larger bisisothioureas complexed to the endothelial NOS heme domain has been determined. These structures afford a structural rationale for the known inhibitory activities. In addition, these structures provide clues on how to exploit the longer inhibitor substituents that extend out of the active site pocket for isoform-selective inhibitor design.

Universal hybridization using LNA (locked nucleic acid) containing a novel pyrene LNA nucleotide monomer.

A novel pyrene LNA nucleotide monomer is shown to mediate universal hybridization when incorporated into a DNA strand or a 2'-OMe-RNA/LNA chimeric strand. For the latter, high-affinity universal hybridization without compromising the base-pairing selectivity of bases neighbouring the universal pyrene LNA nucleotide monomer is documented.

Benefits of lipid lowering on vascular reactivity in patients with coronary artery disease and average cholesterol levels: a mechanism for reducing clinical events?

BACKGROUND: The favorable effects of lowering low-density lipoprotein (LDL)-cholesterol on reducing clinical events in patients with coronary disease have been well established. The mechanisms responsible for this benefit, however, have not been fully understood. This study examined the impact of lipid-lowering therapy on endothelium-dependent vasoreactivity in a subgroup of patients after myocardial infarction with average cholesterol levels who participated in the Cholesterol Recurrent Events (CARE) study to determine whether an effect on endothelial function is a viable mechanism for the observed reduction in clinical events. METHODS AND RESULTS: Participants were recruited from among volunteers in the CARE trial at 2 university-based outpatient cardiology clinics. Patients were randomly assigned to pravastatin or placebo. Plasma lipids were measured at baseline and semiannually thereafter. During the final 6 months of the trial, vasoreactivity was assessed by change in ultrasound-determined brachial artery diameter in response to blood pressure cuff-induced ischemia (endothelium-dependent) and to nitroglycerin, a direct vasodilator. Differences in response were examined between the 2 randomized groups. The relation between change in LDL-cholesterol from baseline to year 5 and the magnitude of endothelium-dependent vasodilation also was examined. There was significantly greater endothelium-dependent vasodilation observed in the pravastatin group compared with the placebo group (13% vs 8%, P =.0002), with no difference between the groups in their response to the endothelium-independent vasodilator nitroglycerin. The magnitude of the endothelium-dependent vasodilation was significantly correlated with the percent change in LDL-cholesterol from baseline to final visit (r = 0.49, P =.015). CONCLUSIONS: These findings indicate that the use of pravastatin in patients after myocardial infarction with average cholesterol levels is associated with greater endothelium-dependent vasodilation compared with those who received placebo. The magnitude of this vasodilatory response is correlated to the reduction in LDL-cholesterol. This improvement in endothelium-dependent vasoreactivity may be a likely mechanism, at least in part, for the reduction in recurrent clinical events observed and reported in the CARE study.

L-arginine binding to nitric-oxide synthase. The role of H-bonds to the nonreactive guanidinium nitrogens.

Nitric-oxide synthase (NOS) catalyzes the oxidation of L-arginine to nitric oxide and L-citrulline. Because overproduction of nitric oxide causes tissue damage in neurological, inflammatory, and autoimmune disorders, design of NOS inhibitors has received much attention. Most inhibitors described to date include a guanidine-like structural motif and interact with the guanidinium region of the L-arginine-binding site. We report here studies with L-arginine analogs having one or both terminal guanidinium nitrogens replaced by functionalities that preserve some, but not all, of the molecular interactions possible for the -NH(2), =NH, or =NH(2)(+) groups of L-arginine. Replacement groups include -NH-alkyl, -alkyl, =O, and =S. Binding of L-canavanine, an analog unable to form hydrogen bonds involving a N(5)-proton, was also examined. From our results and previous work, we infer the orientation of these compounds in the L-arginine-binding site and use IC(50) or K(i) values and optical difference spectra to quantitate their affinity relative to L-arginine. We find that the non-reactive guanidinium nitrogen of L-arginine binds in a pocket that is relatively intolerant of changes in the size or hydrogen bonding properties of the group bound. The individual H-bonds involved are, however, weaker than expected (<2 versus 3-6 kcal). These findings elucidate substrate binding forces in the NOS active site and identify an important constraint on NOS inhibitor design.

Design of isoform-selective inhibitors of nitric oxide synthase.

Nitric oxide synthase, the mammalian enzyme catalyzing the oxidation of L-arginine to L-citrulline and nitric oxide, is present in three isoforms that have distinct physiological roles. Overstimulation or overexpression of individual nitric oxide synthase isoforms plays a role in a wide range of disorders including septic shock, arthritis, diabetes, ischemia-reperfusion injury, pain and various neurodegenerative diseases. Animal studies and early clinical trials suggest that nitric oxide synthase inhibitors could be therapeutic in many of these disorders, but preservation of physiologically important nitric oxide synthase functions might require use of isoform-selective inhibitors. Within the past few years both amino acid and nonamino acid nitric oxide synthase inhibitors with pharmacologically useful isoform selectivity have been reported. Selectivity has been achieved on the basis of initial binding affinity and, for mechanism-based inactivators, on the basis of isoform-dependent catalytic activation; particularly interesting are N5-(1-imino-3-butenyl)-L-ornithine, ARL 17477, 1400W and S-(2-aminoethyl)isothiourea.

N5-(1-Imino-3-butenyl)-L-ornithine. A neuronal isoform selective mechanism-based inactivator of nitric oxide synthase.

Nitric oxide synthase (NOS) catalyzes the NADPH- and O2-dependent conversion of L-arginine to nitric oxide (NO) and citrulline; three isoforms, the neuronal (nNOS), endothelial, and inducible, have been identified. Because overproduction of NO is known to contribute to several pathophysiological conditions, NOS inhibitors are of interest as potential therapeutic agents. Inhibitors that are potent, mechanism-based, and relatively selective for the NOS isoform causing pathology are of particular interest. In the present studies we report that vinyl-L-NIO (N5-(1-imino-3-butenyl)-L-ornithine; L-VNIO) binds to and inhibits nNOS in competition with L-arginine (Ki = 100 nM); binding is accompanied by a type I optical difference spectrum consistent with binding near the heme cofactor without interaction as a sixth axial heme ligand. Such binding is fully reversible. However, in the presence of NADPH and O2, L-VNIO irreversibly inactivates nNOS (kinact = 0.078 min-1; KI = 90 nM); inactivation is Ca2+/calmodulin-dependent. The cytochrome c reduction activity of the enzyme is not affected by such treatment, but the L-arginine-independent NADPH oxidase activity of nNOS is lost in parallel with the overall activity. Spectral analyses establish that the nNOS heme cofactor is lost or modified by L-VNIO-mediated mechanism-based inactivation of the enzyme. The inducible isoform of NOS is not inactivated by L-VNIO, and the endothelial isoform requires 20-fold higher concentrations to attain approximately 75% of the rate of inactivation seen with nNOS. Among the NOS inactivating L-arginine derivatives, L-VNIO is the most potent and nNOS-selective reported to date.

1,2,3-Thiadiazole: a novel heterocyclic heme ligand for the design of cytochrome P450 inhibitors.

The 1,2,3-thiadiazole heterocycle has been explored as a heme ligand and mechanism-based inactivator for the design of cytochrome P450 inhibitors. One 4,5-fused bicyclic and three 4,5-disubstituted monocyclic 1,2,3-thiadiazoles have been examined for their spectral interactions, inhibition, mechanism-based inactivation, and oxidation products by the versatile microsomal P450s 2B4, 2E1, and 1A2. The compounds generally show heteroatom coordination to the heme iron; however, the binding mode is influenced by the architecture of the active site. For example, 4,5-diphenyl-1,2,3-thiadiazole shows type I and type II difference spectra with P450s 2B4 and 2E1, respectively, and no spectral perturbation with P450 1A2. Except for the fused bicyclic compound, the spectral dissociation constants are in the 2-50 microM range. The effectiveness as an inhibitor depends on the substituents at the 4- and 5- positions and on the P450 examined. Inhibition of the P450-catalyzed 1-phenylethanol oxidation to acetophenone by the thiadiazoles does not correlate with either the type of binding spectra or the spectral dissociation constants of the compounds. P450s 2E1 and 2B4 are inactivated by the 4,5-fused bicyclic 1,2,3-thiadiazole in a mechanism-based manner. Inactivation of the P450 correlates with loss in absorbance at 450 nm for the ferrous-CO complex. The monocyclic 1,2,3-thiadiazoles do not inactivate any of the P450s examined. The 1,2,3-thiadiazole ring is oxidized by the P450 system. Oxidation of the monocyclic compounds results in extrusion of the three heteroatoms and formation of the corresponding acetylenes, whereas oxidation of the fused bicyclic compound does not yield an acetylenic product.

Simultaneous determination of native and subunit molecular weights of proteins by pore limit electrophoresis and restricted use of sodium dodecyl sulfate.

In the present communication, we describe a method for the determination of both the native and subunit molecular weight of a protein by a single pore limit electrophoretic run. When native proteins and sodium dodecyl sulfate (SDS)-heat denatured proteins were electrophoresed in a 4-28% gradient-polyacrylamide gel, in the presence of 0.02% SDS in running buffer, their respective molecular weights (native and subunit) could be determined by comparing the migration distances of unknown and standard proteins. The presence of SDS up to 0.02% in the running buffer did not dissociate the native proteins into their subunits. The linearity in distribution of native and SDS-polyacrylamide gel electrophoresis (PAGE) standard marker proteins used for the molecular weight determination further showed the efficacy of the present technique.

Hierarchical gene diversity and genetic structure of tribal populations of Andhra Pradesh, India.

Gene diversity and genetic structure of tribal populations of Andhra Pradesh, India, have been analyzed under a hierarchical model consisting of five regions of the state, tribes within the regions, and local subpopulations within the tribes. Average gene diversity has been estimated from gene frequency data for 15 polymorphic loci by using nested gene diversity analysis of GST. The intralocation coefficient of gene diversity was estimated at 96% of the total, whereas the intertribal, within--and between--regional gene diversities were found to be only 1.90, 0.95, and 1.43%, respectively. The estimate of gene diversity was higher for loci with higher degrees of polymorphism such as ABO, MN, ESD, and PTC and lower for loci with low-level polymorphism and extreme gene frequencies such as Hb, Tf, PHI, 6PGD, and Hp. The nature of selective preference or neutrality at the loci seems to be important in this respect. Tribes of the plains exhibit the least gene diversity, apparently because of higher gene flow among them. The contribution of loci with intermediate gene frequencies in intertribal and regional gene diversity was found to be higher than for loci with extreme allelic frequencies. These results suggest that the most significant component of variation is between individuals within locations and that variation between local subpopulations is negligible in the genetic structure of a population. Forces like selection, gene flow and drift also influence the diversity depending upon the nature of the locus.

Evidence for autophosphorylation of hyaluronate binding protein and its enhanced phosphorylation in rat histiocytoma.

This report documents for the first time the in vitro autophosphorylation of purified 68 kDa hyaluronate binding protein in presence of [32P] ATP. The rate of phosphorylation is proportional to the concentration of protein and to the time of incubation up to 5 min. By both phosphoamino acid and western blot analysis with antiphosphotyrosine antibodies, we have confirmed that the phosphorylation occurs at tyrosine residues. Immunoprecipitation with anti HA binding protein antibody shows a 5 fold increase in the phosphorylation in macrophage histiocytoma compared to normal macrophage. Supplementing hyaluronate with hyaluronate binding protein in the medium is further shown to enhance total protein phosphorylation in rat histiocytoma.

Studies of novel pentacyclic heterocyclic steroids: Part XXI. Total synthesis of racemic benz[3,4]-6-oxaestra-1,3,5(10),8-tetraen-17 beta-ol.

1-Oxo-4-oxa-1,2,3,4-tetrahydrophenanthrene is converted into racemic benz[3,4]-6-oxaestra-1,3,5(10),8-tetraen-17 beta-ol in 45% yield.