Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules

Evolutionary approaches are regularly used to isolate single molecules with desired activities from large populations of nucleic acids (approximately 10(15)). Several methods have also been developed to generate libraries of mRNA-encoded peptides and proteins for the in vitro selection of functional polypeptides. In principal, such mRNA encoding systems could be used with libraries of nonbiological polymers if the ribosome can be directed to polymerize tRNAs carrying unnatural amino acids. The fundamental problem is that current chemical aminoacylation systems cannot easily produce sufficient amounts of the numerous misacylated tRNAs required to synthesize a complex library of encoded polymers. Here, we show that bulk-aminoacylated tRNA can be transformed into N-monomethylated aminoacyl tRNA and translated. Because poly-N-methyl peptide backbones are refractory to proteases and are membrane permeable, our method provides an uncomplicated means of evolving novel drug candidates.     

Enthalpic relaxation of convective desiccated trehalose-water glasses

Minimizing molecular mobility for desiccation preservation of biologics close to ambient temperature using trehalose glasses require quantitative characterization of their enthalpic relaxation at various end water contents. Differential scanning calorimetry (DSC) was used to characterize three different water contents: 0%, 1.5% and 10% over a wide range of aging temperatures. Results showed the characteristic time (τ) varies both with the water content and the aging temperature. τ increased with lowered aging temperature but showed a non-monotonous relationship as a function of water content. Fragility of trehalose glasses was analyzed using thermophysical parameters obtained from relaxation studies. The study showed trehalose to be a fragile glass former at all water contents, with 0% water samples showing a relatively stronger glass. A compromise between molecular mobility and glass fragility led to an optimal water content close to 1.5% and an aging temperature close to room temperature. This would ensure a τ value of 9000 h, which corresponds to a storage period of a year.     

Synthesis of racemic cis-5-hydroxy-3-phthalimidoglutarimide. A metabolite of thalidomide isolated from human plasma

[reaction: see text] A synthesis of the glutarimide-derived metabolite of thalidomide, 5'-hydroxythalidomide (2), is described. The synthesis employed the lactone derivative of N-benzyloxycarbonyl (CBZ)-protected 4-hydroxyglutamic acid 12, which is prepared by a de novo route from diethyl acetamidomalonate. The reaction of 12 with 4-methoxybenzylamine gave the corresponding isoglutamine, which then provided the key CBZ-protected N-PMB-glutarimide 14 after dehydration. Deprotection of both the CBZ and PMB groups followed by phthalimidation and deacetylation of the 3-amino-5-acetoxyglutarimide 16 afforded 2.     

Stereoselective syntheses of highly functionalized bicyclo[3.1.0]hexanes: a general methodology for the synthesis of potent and selective mGluR2/3 agonists

[Chemical reaction: See text] A Et3Al mediated intramolecular epoxide opening, cyclopropanation reaction is described. The transformation provided highly functionalized bicyclo[3.1.0]hexane systems in high efficiency and with perfect H or F endo selectivity. Application of this reaction to the synthesis of mGluR2/3 agonist 1 (43% overall yield) and a few intermediates suitable for the synthesis of other bicyclo[3.1.0]hexane mGluR2/3 agonists is discussed.     

Hyperfine fields in the 5sp series studied by the low temperature nuclear orientation of83Rb,83Sr,85Sr and85Ym in iron

The hyperfine fields B_hf (RbFe), B_hf (SrFe) and B_hf (YFe) have been determined by the low temperature nuclear orientation of dilute samples of⁸³Rb,^83,85Sr and⁸⁵Y^m in an iron lattice to be B_hf (RbFe)=+54 (10) kG, B_hf (SrFe)=(?)100 (30) kG and B_hf (YFe)=?226 (10) kG. These results are compared with recent calculations for these fields (1), (2).     

Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold

The efficiency of fluorescence resonance energy transfer (FRET) between two chromophores positioned at opposite ends of DNA base pair domains has been investigated. The base pair domain serves as a helical scaffold which defines both the distance between chromophores and the dihedral angle between their electronic transition dipole moments, each incremental base pair increasing the distance and stepping the dihedral angle. Fluorescence quantum yields and lifetimes have been determined for both the donor and acceptor chromophores. The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipole model conventionally assumed for FRET.     

Should dithiophosphinate esters function as RAFT agents?

[graph: see text] High-level ab initio calculations indicate that *CH3 addition to the sulfur center of S=P(Z)(Z')SCH3 (Z,Z' = CH3, CN, OCH3, Ph) is considerably less exothermic than addition to the corresponding RAFT agents, S=C(Z)SCH3. This suggests that dithiophosphinate esters may have only limited use in controlling free-radical polymerization, but should make excellent radical chain carriers in organic synthesis. The results cast doubt on the notion that phosphoranyl radicals are more "intrinsically" stabilized than carbon-centered radicals.     

Structures and cytotoxic properties of sponge-derived bisannulated acridines

A reinvestigation of sponge natural products from additional Indo-Pacific collections of Xestospongiacf. carbonaria and X. cf. exigua has provided further insights on the structures, biological activities, and biosynthetic origin of bisannulated acridines. These alkaloids include one known pyridoacridine, neoamphimedine (2), and three new analogues, 5-methoxyneoamphimedine (4), neoamphimedine Y (5), and neoamphimedine Z (6). A completely new acridine, alpkinidine (7), was also isolated. A disk diffusion soft agar assay, using a panel of five cancer cell lines (solid tumors and leukemias) and two normal cells, was used to evaluate the differential cytotoxicity (solid tumor selectivity) of the sponge semipure extracts and selected compounds including amphimedine (1), 2, 4, and 7. While all four compounds were solid tumor selective, 1 and 2 were the most potent and 4 was the most selective. The rationale used to characterize the new structures is outlined along with the related biosynthetic pathways envisioned to generate 2 and 7.     

Theoretical study of the spin trapping of hydroxyl radical by cyclic nitrones: a density functional theory approach

The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.     

An unexpected symmetry of the coulomb potential in the debye-smoluchowski equation

Generalised diffusion processes are discussed using the theory of stochastic processes and several elementary results are proved for the survival probability of a pair of particles with an arbitrary potential. The reaction probability conditioned on reaction ultimately occurring is considered and its backward equation is determined. In the case of the Coulomb potential the probability is shown analytically to be identical in both the attractive and repulsive cases for a given absolute value of r_c. The utility of this result in numerical solutions of the Debye—Smoluchowski equation is discussed.