Hydrogen-atom abstraction from the adenine-uracil base pair

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.     

BORAZANs: tunable fluorophores based on 2-(pyrazolyl)aniline chelates of diphenylboron

The reaction between 2-pyrazolyl-4-X-anilines, H(pzAnX), (X = para-OMe (L1), Me (L2), H (L3), Cl (L4), CO2Et (L5), CF3 (L6), CN (L7)) and triphenylboron in boiling toluene affords the respective, highly emissive N,N'-boron chelate complexes, BPh2(pzAnX) (X = para-OMe (1), Me (2), H (3), Cl (4), CO2Et (5), CF3 (6), CN (7)) in high yield. The structural, electrochemical, and photophysical properties of the new boron complexes can be fine-tuned by varying the electron-withdrawing or -donating power of the para-aniline substituent (delineated by the substituent's Hammett parameter). Those complexes with electron-withdrawing para-aniline substituents such as CO2Et (5), CF3 (6), and CN (7) have more planar chelate rings, more 'quinoidal' distortion in the aniline rings, greater chemical stability, higher oxidation potentials, and more intense (phiF = 0.81 for 7 in toluene), higher-energy (blue) fluorescent emission compared to those with electron-donating substituents. Thus, for 1 the oxidation potential is 0.53 V versus Ag/AgCl (compared to 1.12 V for 7), and the emission is tuned to the yellow-green but at an expense in terms of lower quantum yields (phiF = 0.07 for 1 in toluene) and increased chemical reactivity. Density functional calculations (B3LYP/6-31G*) on PM3 energy-minimized structures of the ligands and boron complexes reproduced experimentally observed data and trends and provided further insight into the nature of the electronic transitions.     

A real-time,fluorescence-based assay for Rho-associated protein kinase activity

Inhibitors of Rho-associated protein kinase (ROCK) enzymatic activity have been shown to reduce the invasive phenotype observed in metastatic hepatocellular carcinoma (HCC). We describe the design, synthesis, and evaluation of a direct probe for ROCK activity utilizing a phosphorylation-sensitive sulfonamido-oxine fluorophore, termed Sox. The Sox fluorophore undergoes an increase in fluorescence upon phosphorylation of a proximal amino acid via chelation-enhanced fluorescence (CHEF, ex. = 360 nm and em. = 485 nm), allowing for the direct visualization of the rate of phosphate addition to a peptide substrate over time. Our optimal probe design, ROCK-S1, is capable of sensitively reporting ROCK activity with a limit of detection of 10 pM and a high degree of reproducibility (Z’-factor = 0.6 at 100 pM ROCK2). As a proof-of-principle for high-throughput screening (HTS) we demonstrate the ability to rapidly assess the efficacy of a 78 member, small molecule library against ROCK2 using a robotics platform. We identify two previously unreported ROCK2 inhibitor scaffolds, PHA665752 and IKK16, with IC₅₀ values of 3.6 μM and 247 nM respectively. Lastly, we define conditions for selectively monitoring ROCK activity in the presence of potential off-target enzymes (PKCα, PKA, and PAK) with similar substrate specificities.     

High-Dimensional Menger-Type Curvatures—Part II: d-Separation and a Menagerie of Curvatures

We estimate d-dimensional least squares approximations of an arbitrary d-regular measure μ via discrete curvatures of d+2 variables. The main result bounds the least squares error of approximating μ (or its restrictions to balls) with a d-plane by an average of the discrete Menger-type curvature over a restricted set of simplices. Its proof is constructive and even suggests an algorithm for an approximate least squares d-plane. A consequent result bounds a multiscale error term (used for quantifying the approximation of μ with a sufficiently regular surface) by an integral of the discrete Menger-type curvature over all simplices. The preceding paper (part I) provided the opposite inequalities of these two results. This paper also demonstrates the use of a few other discrete curvatures which are different from the Menger-type curvature. Furthermore, it shows that a curvature suggested by Léger (Ann. Math. 149(3), pp. 831–869, 1999) does not fit within our framework.     

Transition state analogue discrimination by related purine nucleoside phosphorylases

Transition state analogues of PNP, the Immucillins and DADMe-Immucillins, were designed to match transition state features of bovine and human PNPs, respectively. The inhibitors with or without the hydroxyl and hydroxymethyl groups of the substrate demonstrate that inhibitor geometry mimicking that of the transition state confers binding affinity discrimination. This finding is remarkable since crystallographic analysis indicates complete conservation of active site residues and contacts to ligands in human and bovine PNPs.