The statistical significance of selected sense–antisense peptide interactions

Sense and antisense peptides, encoded by sense and corresponding antisense DNA strands, are capable of specific interactions that could be a driving force to mediate protein–protein or protein–peptide binding associations. The complementary residue hypothesis suggests that these interactions are founded upon the sum of pairwise interactions between amino acids encoded by corresponding sense and antisense codons. Despite many successful experimental results obtained with the hypothesis, however, the physicochemical basis for these interactions is poorly understood. We examined the potential of the hypothesis for general identification of protein–protein interaction sites, and the possible role of the hypothesis in determining folding in a broad set of protein structures. In addition, we performed a structural study to investigate the binding of a complementary peptide to IL‐1F2. Our results suggest that complementary residue pairs are no more frequent or conserved than average in protein–protein interfaces, and are statistically under‐represented amongst contacting residue pairs in folded protein structures. Although our structural results matched experimental observations of binding between the peptide and IL‐1F2, complementary residue interactions do not appear to be dominant in the bound structure. Overall, our data do not allow us to conclude that the complementary residue hypothesis accounts for specific sense–antisense peptide interactions. © 2012 Wiley Periodicals, Inc.     

Stable Quinome Methides: Regioselective Para-Oxidation of a 2,4-Bisalkylthiomethenol and Addition Reaction Reaction to Quinonemethides

Abstract

The 2.4-bisfunctionalized phenol 1, a commercial antioxidant, is dehydrogenated regioselectively with potassium ferricyanide. affording the corresponding p-quinone methide 2. 1,6-Addition of nucleophiles e.g. thiols to 2 gives rise to the corresponding addition products e.g. the dithioacetals 4 of the corresponding substituted benzaldehyde. On the other hand, treatment of 2 with αα′-azoisobutyronitrile at 90°C leads to compounds 5a-b and 6, addition products of the cyanopropyl radical to the quinone methide 2. The structures of all products are confirmed mainly by ¹H-NMR-and ¹³C-NMR-spectroscopy and the mode of their formation is discussed.     

TBD-Catalyzed Trifluoromethylation of Carbonyl Compounds with (Trifluoromethyl)trimethylsilane

Trifluoromethylation of carbonyl compounds using (trifluoromethyl) trimethylsilane catalyzed by 1,5,7-triazabicyclo[4,4,0]dec-5-ene (TBD) afforded the corresponding α-trifluoromethyl alcohols in good to excellent yields under mild reaction conditions.

Supplemental materials are available for this article. Go to the publisher's online edition of Synthetic Communications® to view the free supplemental file.     

Metal‐Ion‐Binding Analogs of Ribonucleosides: Preparation and Formation of Ternary Pd2+ and Hg2+ Complexes with Natural Pyrimidine Nucleosides

Four metal‐ion‐binding nucleosides, viz. 2,6‐bis(1‐methylhydrazinyl)‐9‐(β‐D ‐ribofuranosyl)‐9H‐purine ( 2a ) and its N‐acetylated derivative, 2b , 2,4‐bis(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)‐5‐(β‐D ‐ribofuranosyl)pyrimidine ( 3 ), and 2,4‐bis(1‐methylhydrazinyl)‐5‐(β‐D ‐ribofuranosyl)pyrimidine ( 4 ) have been synthesized. The ability of these nucleosides and the previously prepared 2,6‐bis(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)‐9‐(β‐D ‐ribofuranosyl)‐9H‐purine to form Pd²⁺‐ and Hg²⁺‐mediated complexes with uridine has been studied by ¹H‐NMR spectroscopy. To obtain additional support for the interpretation of the NMR data, comparative measurements on the ternary‐complex formation between pyridine‐2,6‐dicarboxamide ( 5 ), pyrimidine nucleosides, and K₂PdCl₄ were carried out.     

Supramolecular organogelators based on Janus type AT nucleosides

J-AT nucleoside-based organogelators 1a and 1b were designed and synthesized. They were endowed with unparalleled superiority to natural nucleobase analogues 2–6 to gelate aromatic solvents due to their excellent self-assembly properties. The J-AT nucleoside-based organogelators showed a specific self-complementary base pair recognition characteristic. The gel stabilities of 1a and 1b were drastically influenced by adenine analogue 2, hardly affected by thymine analogue 3, uracil analogue 4, cytosine analogue 5, and mildly interrupted by guanine analogue 6.     

Thermosensitive Gels for the Topical Administration of Diltiazem

In the present work, thermosensitive systems were prepared, characterized, and proposed for diltiazem administration in the topical treatment of anal fissures. Methylcellulose and PluronicF127 were used as gelling polymers. Some low-toxicity molecules, such as sodium glycocholate, citric acid, and lactic acid, were added to gel formulations as counterions to enhance diltiazem lipophilicity. The systems were characterized by sol-gel transition temperature, viscosity, and rheological studies. The resulting data allowed us to determine which systems presented sol-gel transition. A change from Newtonian to plastic behavior at sol-gel transition temperature was observed. An increase in diltiazem pig skin permeability and two-fold skin accumulation was observed in the presence of citric acid.     

Chirality Induction by Formation of Assembled Structures Based on Anion‐Responsive π‐Conjugated Molecules

Anion‐responsive π‐conjugated compounds having chiral alkyl chains were synthesized. Circular dichroism (CD) and circularly polarized luminescence (CPL) were observed in the solution‐state assemblies of the chiral anion receptors and those of their anion complexes as salts of a planar triazatriangulenium cation. The CD and CPL spectral patterns of the ion‐pair‐based assemblies were completely opposite to those of the anion‐free assemblies, and this suggests that anion binding and subsequent ion pairing change the chirality of the assembly modes.     

Reactivity Studies of Iridium Pyridylidenes [TpMe2Ir(C6H5)2(C(CH)3C(R)NH] (R=H,Me, Ph)

The reactivity of a series of iridium? pyridylidene complexes with the formula [Tp^Me2Ir(C₆H₅)₂(C(CH)₃C(R)N H] ( 1 a – 1 c ) towards a variety of substrates, from small molecules, such as H₂, O₂, carbon oxides, and formaldehyde, to alkenes and alkynes, is described. Most of the observed reactivity is best explained by invoking 16 e^? unsaturated [Tp^Me2Ir(phenyl)(pyridyl)] intermediates, which behave as internal frustrated Lewis pairs (FLPs). H₂ is heterolytically split to give hydride? pyridylidene complexes, whilst CO, CO₂, and H₂C?O provide carbonyl, carbonate, and alkoxide species, respectively. Ethylene and propene form five‐membered metallacycles with an IrCH₂CH(R)N (R=H, Me) motif, whereas, in contrast, acetylene affords four‐membered iridacycles with the IrC(?CH₂)N moiety. C₆H₅(C?O)H and C₆H₅C?CH react with formation of Ir? C₆H₅ and Ir? C?CPh bonds and the concomitant elimination of a molecule of pyridine and benzene, respectively. Finally the reactivity of compounds 1 a – 1 c against O₂ is described. Density functional theory calculations that provide theoretical support for these experimental observations are also reported.