Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

A Schiff base expanded porphyrin macrocycle that acts as a versatile binucleating ligand for late first-row transition metals

The coordination chemistry of the Schiff base polypyrrolic octaaza macrocycle 1 toward late first-row transition metals was investigated. Binuclear complexes with the divalent cations Ni(II), Cu(II), and Zn(II) and with the monovalent cation Cu(I) were prepared and characterized. Air oxidation of the Cu(I) ions in the latter complex to their divalent oxidation state resulted in a change in the coordination mode relative to the macrocycle.     

The boron-catalyzed polymerization of dimethylsulfoxonium methylide. A living polymethylene synthesis

Trialkyl and aryl organoboranes catalyze the polymerization of dimethylsulfoxonium methylide (1). The product of the polymerization is a tris-polymethylene organoborane. Oxidation affords linear telechelic alpha-hydroxy polymethylene. The polymer molecular weight was found to be directly proportional to the stoichiometric ratio of ylide/borane, and polydispersities as low as 1.01-1.03 have been realized. Although oligomeric polymethylene has been the most frequent synthetic target of this method, polymeric star organoboranes with molecular weights of 1.5 million have been produced. The average turnover frequency at 120 degrees C in 1,2,4,5-tetrachlorobenzene/toluene is estimated at >6 x 10(6) g of polymethylene (mol boron)(-1) h(-1). The mechanism of the polyhomologation reaction involves initial formation of a zwitterionic organoborane.ylide complex which breaks down in a rate-limiting 1,2-alkyl group migration with concomitant expulsion of a molecule of DMSO. The reaction was found to be first order in the borane catalyst and zero order in ylide. DMSO does not interfere with the reaction. The temperature dependence of the reaction rate yielded the following activation energy parameters (toluene, DeltaH(++) = 23.2 kcal/mol, DeltaS(++) = 12.6 cal deg/mol, DeltaG(++) = 19.5 kcal/mol; THF, DeltaH(++) = 26.5 kcal/mol, DeltaS(++) = 21.5 cal deg/mol, DeltaG(++) = 20.1 kcal/mol).     

The Crystal Structure of Ba3Cu2Al2F16: a Relative of Ba4Cu2Al3F21

Ba₃Cu₂Al₂F₁₆ is monoclinic: a = 7.334(1)Å, b = 5.320(2)Å, c = 16.022(1)Å, β = 96.34(1)°, Z = 2. Its crystal structure was solved in the space group P2₁ (No. 4) from synchrotron X‐ray single crystal data using 2685 unique reflections (2639 with F_o/σ(F_o) > 4). The final R factor is 0.044. The structure consists of a succession along the c‐axis of the cell of three layers of two different kinds of sheets developing in the (a, b) plane. The first one, formulated [(AlF₅)₂]_∞^4— and hereafter named A, is built up from infinite cis‐chains of aluminium‐fluorine octahedra [AlF₆], linked by two vertices and distanced by a. The second one, formulated [Cu₂AlF₁₁]_∞^4— and named B, is bidimensional. It is constituted of distorted copper‐fluorine octahedra [CuF₆], linked by edges, which form infinite chains interconnected by three vertices of isolated [AlF₆] octahedra. The stacking sequence of the sheets is (A, B, B)_∞. The barium ions, 12‐coordinated, are inserted between the sheets. The crystal structure of Ba₃Cu₂Al₂F₁₆ is closely related to that of Ba₄Cu₂Al₃F₂₁. Only the proportion and the stacking sequence of the two kinds of sheets in the c‐direction differ, according to two different compositions and two different symmetries.     

Hydrolysis of cellobiose by immobilized β-glucosidase entrapped in maintenance-free gel spheres

A crude preparation of Aspergillus niger β-glucosidase (27.5 cello-biase U/mg protein at 40°C, pH 5.0) was immobilized on concanavalin A-Sepharose (CAS). The cellobiase activity of the immobilized enzyme was 1334 U/mg dried CAS or 108 U/mL CAS gel. The β-glucosidase-CAS complex was entrapped within crosslinked propylene glycol alginate/bone-geletin gel spheres that possessed between 0.67 and 2.35 cellobiase U/mL spheres, depending on their size. The effect of cellobiose concentration (10–300 mM) on the activity of native, immobilized, and gel-entrapped enzyme was determined. It was shown that concentrations of cellobiose between 10 and 180 mM were not inhibitory to the entrapped enzyme, although inhibition was found to occur with the native and immobilized enzyme. Exogenous ion addition was not necessary to maintain the structural integrity of the spheres, which were stable for 4 d at 40°C.     

A note on the nonexistence of Barker sequences

A Barker sequence is a sequence with elements ±1 such that all out-of-phase aperiodic autocorrelation coefficients are 0, 1 or -1. It is known that if a Barker sequence of length s > 13 exists then s = 4N ² for some odd integer N 55, and it has long been conjectured that no such sequence exists. We review some previous attempts to improve the bound on N which, unfortunately, contain errors. We show that a recent theorem of Eliahou et al. [5] rules out all but six values of N less than 5000, the smallest of which is 689.     

Asymmetric synthesis of (1R,2S,3R)-3-methylcispentacin and (1S,2S,3R)-3-methyltranspentacin by kinetic resolution of tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate

Conjugate addition of lithium dibenzylamide to tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate occurs with high levels of stereocontrol, with preferential addition of lithium dibenzylamide to the face of the cyclic alpha,beta-unsaturated acceptor anti- to the 3-methyl substituent. High levels of enantiorecognition are observed between tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate and an excess of lithium (+/-)-N-benzyl-N-alpha-methylbenzylamide (10 eq.) (E > 140) in their mutual kinetic resolution, while the kinetic resolution of tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate with lithium (S)-N-benzyl-N-alpha-methylbenzylamide proceeds to give, at 51% conversion, tert-butyl (1R,2S,3R,alphaS)-3-methyl-2-N-benzyl-N-alpha-methylbenzylaminocyclopentane-1-carboxylate consistent with E > 130, and in 39% yield and 99 +/- 0.5% de after purification. Subsequent deprotection by hydrogenolysis and ester hydrolysis gives (1R,2S,3R)-3-methylcispentacin in > 98% de and 98 +/- 1% ee. Selective epimerisation of tert-butyl (1R,2S,3R,alphaS)-3-methyl-2-N-benzyl-N-alpha-methylbenzylaminocyclopentane-1-carboxylate by treatment with KO'Bu in 'BuOH gives tert-butyl (1S,2S,3R,alphaS)-3-methyl-2-N-benzyl-N-alpha-methylbenzylaminocyclopentane-1-carboxylate in quantitative yield and in > 98% de, with subsequent deprotection by hydrogenolysis and ester hydrolysis giving (1S,2S,3R)-3-methyltranspentacin hydrochloride in > 98% de and 97 +/- 1% ee.     

Measurement of nitric oxide by 4,5-diaminofluorescein without interferences

The fluorescent reagent 4,5-diaminofluorescein (DAF-2) has been widely used for specific and quantitative measurements of nitric oxide (NO) in biological tissues. Recently it was reported that dehydroascorbic acid (DHA) and ascorbic acid (AA) interfere with the measurement of NO using DAF-2. A new method of assaying NO using DAF-2 eliminates these interferences; when frozen on dry ice, the NO in the original solution still diffuses and can react with an adjacent frozen block of DAF-2, but the confounding compounds such as DHA do not. Thus, placing the microliter-volume frozen blocks of solutions containing NO and the solutions of DAF-2 adjacent to each other for 30 min results in the concentration dependent formation of fluorescent product (DAF-2T) from the reaction of NO with DAF-2. The product has been characterized and the method validated using both fluorescence spectroscopy and capillary electrophoresis with laser induced fluorescence detection. With this approach, the presence of DHA and AA does not interfere with NO measurements, and product formation is inhibited in the presence of NO scavengers added to either of the solutions before freezing. The contactless DAF-2 method successfully assays NO in nitric oxide synthase-positive vertebrate and invertebrate tissues. This method allows nondestructive NO detection in biological samples that can subsequently be used for morphological and/or biochemical studies.     

Swallowtail porphyrins: synthesis, characterization and incorporation into porphyrin dyads

The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.     

Missing-link macrocycles: hybrid heterocalixarene analogues formed from several different building blocks

The synthesis and structural characterization of hybrid heterocalix[4]arene analogues containing pyrrole, benzene, methoxy-substituted benzene, and pyridine subunits is described. Macrocycles 1 and 2, examples of calix[2]benzene[2]pyrrole and calix[1]benzene[3]pyrrole systems, respectively, are synthesized by the condensation of pyrrole and an appropriate phenylbis(carbinol). Macrocycles 3 and 7, examples of calix[2]benzene[1]pyridine[1]pyrrole and calix[1]pyridine[3]pyrrole, respectively, are synthesized by the use of a carbene-based pyrrole-to-pyridine ring-expansion procedure. Single-crystal X-ray analysis reveals that compounds 1a, 1b, and 2b adopt 1,3-alternate conformations in the solid state, whereas compounds 3 and 7 display structures that are best described as "flattened partial cones" in terms of their conformation. (Series a refers to pure benzene-derived systems, whereas series b indicates macrocycles containing 5-methoxyphenyl subunits). In the solid state, the methoxy-functionalized macrocycles 1b and 2b, and the chloropyridine-containing macrocycle 7 exist as dimers. In the case of 1a and 7, these compounds interact with neutral solvent in the solid state. The conformations of the macrocycles in solution were explored by temperature-dependent proton NMR and NOESY spectral analysis. At 188 K, macrocycles 1a and 2a adopt flattened 1,3-alternate conformations, whereas macrocycles 3 and 7 exist in the form of flattened partial-cone conformations. Standard proton NMR titration analyses were carried out in the case of macrocycles 1a and 2a, and reveal that at least the second of these systems is capable of binding fluoride and chloride anions in CD(2)Cl(2) solution at room temperature (K(a)=571 and 17M(-1) in the case of 2a and F(-) and Cl(-), respectively).