Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) tethering a Hoechst 33258 analogue: triplex and duplex stabilization by simultaneous minor groove binding

Deoxynucleic guanidine (DNG), a DNA analogue in which positively charged guanidine replaces the phosphodiester linkages, tethering to Hoechst 33258 fluorophore by varying lengths has been synthesized. A pentameric thymidine DNG was synthesized on solid phase in the 3' --> 5' direction that allowed stepwise incorporation of straight chain amino acid linkers and a bis-benzimidazole (Hoechst 33258) ligand at the 5'-terminus using PyBOP/HOBt chemistry. The stability of (DNA)(2).DNG-H triplexes and DNA.DNG-H duplexes formed by DNG and DNG-Hoechst 33258 (DNG-H) conjugates with 30-mer double-strand (ds) DNA, d(CGCCGCGCGCGCGAAAAACCCGGCGCGCGC)/d(GCGGCGCGCGCGCTTTTTGGGCCGCGCGCG), and single-strand (ss) DNA, 5'-CGCCGCGCGCGCGAAAAACCCGGCGCGCGC-3', respectively, has been evaluated by thermal melting and fluorescence emission experiments. The presence of tethered Hoechst ligand in the 5'-terminus of the DNG enhances the (DNA)(2).DNG-H triplex stability by a DeltaT(m) of 13 degrees C. The fluorescence emission studies of (DNA)(2).DNG-H triplex complexes show that the DNG moiety of the conjugates bind in the major groove while the Hoechst ligand resides in the A:T rich minor groove of dsDNA. A single G:C base pair mismatch in the target site decreases the (DNA)(2).DNG triplex stability by 11 degrees C, whereas (DNA)(2).DNG-H triplex stability was decreased by 23 degrees C. Inversion of A:T base pair into T:A base pair in the center of the binding site, which provides a mismatch selectively for DNG moiety, decreases the triplex stability by only 5-6 degrees C. Upon hybridization of DNG-Hoechst conjugates with the 30-mer ssDNA, the DNA.DNG-H duplex exhibited significant increase in the fluorescence emission due to the binding of the tethered Hoechst ligand in the generated DNA.DNG minor groove, and the duplex stability was enhanced by DeltaT(m) of 7 degrees C. The stability of (DNA)(2).DNG triplexes and DNA.DNG duplexes is independent of pH, whereas the stability of (DNA)(2).DNG-H triplexes decreases with increase in pH.     

Ruthenium(III)- and osmium(VIII)-catalyzed oxidation of 2-thiouracil by bromamine-B in acid and alkaline media: a kinetic and mechanistic study

The kinetics of oxidation of 2-thiouracil (TU) by sodium N-bromobenzenesulphonamide or bromamine-B (BAB) have been studied in an HCl medium, catalyzed by RuCl₃, and in a NaOH media with OsO₄ as catalyst, at 313 K. The stoichiometry and oxidation products are the same in both cases, but their kinetic patterns were found to be different. In acid medium the rate shows a first order dependence in each of [BAB] and [TU], and is dependent on [Ru^III]. The reaction rate is inversely dependent on [H⁺]. In alkaline medium, the rate is first order in [BAB] and in [Os^VIII] and zero order in [TU]. The reaction rate is dependent on [NaOH]. Activation parameters have been evaluated, solvent isotope effects have been studied in D₂O medium, and equilibrium constants were calculated. The activation parameters and rate constants indicate that the catalytic efficiency is: Os^VIII > Ru^III. The proposed mechanisms and the derived rate laws are consistent with the observed kinetics.     

Sequence selective recognition in the minor groove of dsDNA by pyrrole,imidazole-substituted bis-benzimidazole conjugates

A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.     

Preparation of (1R,4S)-4-hydroxycyclopent-2-en-1-yl acetate via Novozym-435® catalyzed desymmetrization of cis-3,5-Diacetoxy-1-cyclopentene

Photooxidation of cyclopentadiene has been carried out in methanol using white light of LED lamp, rose bengal as photo initiator, and compressed air at 0?°C. Under conditions of [thiourea] ? [cyclopentadiene], the consumption of thiourea follows a pseudo-first-order reaction kinetics with half life of 75?±?10?min; corr. coeff. r?=?0.989. Slow addition of the monomer and maintaining excess thiourea concentration in reaction mass improves the yield. cis-3,5-Dihydroxy-1-cyclopentene is acetylated without isolation to obtain cis-3,5-Diacetoxy-1-cyclopentene of high purity (>99%) with overall isolated yield of 30%. Desymmetrization of the diacetate to (1R,4S)-4-hydroxycyclopent-2-en-1-yl acetate has been carried out via enzymatic transesterification with methanol in methyl tert-butyl ether (MTBE) at 5?°C using Novozym-435^®. The enantiomerically pure monoacetate (e.e. >99%) was obtained in 95% isolated yield. The recovered enzyme was reused for more than 10 times without loss in yield and selectivity. The entire protocol does not require purification of final product by chromatography.     

The facile and efficient organocatalytic platform for accessing 1,2,4-selenadiazoles and thiadiazoles under aerobic conditions

The first organocatalytic approach towards synthesis of rarely explored 1,2,4-selenadiazole and thiadiazole scaffolds have been devised using corresponding carboxamides as substrates. The transformations were realized using two distinct conditions in the presence of catalytic vitamin B₃ or thiourea under aerobic conditions. Developed methods overcome the associated limitations of previous reported approaches and the desired products were obtained in high yields and selectivity without the formation of toxic side-products.     

Ruthenium(III)-catalyzed oxidation of substituted ethanols by sodium N-bromo-p-toluenesulfonamide in hydrochloric acid medium

The kinetics of oxidation of substituted alcohols, RCH2CH2OH (R = H-, OEt-, OMe-, NH2-, Cl- and Br-) by sodium N-bromo-p-toluenesulfonamide or bromamine-T (BAT), catalyzed by ruthenium(III) chloride in the presence of HCl, has been studied at 303K. The reaction rate shows first order dependence each on [BAT], [alcohol] and [RuIII]. The reaction rate is inversely dependent on [H+]. Addition of halide ions and the reduction product, p-toluenesulfonamide has no significant effect on the rate. Composite activation parameters H, S and G were computed by studying the reaction at different temperatures (298–313K). The rate decreased in D2O medium and the solvent isotope effect k(H2O)|k(D2O) = 1.63 and 1.68 for EtOH and BrCH2CH2OH respectively. Proton inventory studies have been made in H2O–D2O mixtures for both alcohols. The conjugate acid, TsNHBr, is assumed to be the reactive species. The rates do not correlate satisfactorily with Taft substituent constants. The protonation constant (25.3) of monobromamine-T has been evaluated. From enthalpy-entropy relationships and Exner correlations, the isokinetic temperature () was found to be 368 K, which is much higher than the experimental temperature, indicating that enthalpy factors control the rate. The proposed reaction mechanisms and the derived rate laws are consistant with the observed kinetic data. The rate of oxidation of alcohols RCH2CH2OH follows the order: H > Br > OEt > OMe > Cl > NH2.     

Synthesis of Phenyl or 4-Nitrophenyl Methyl β-Ketophosphonate Esters

Seven new aryl methyl g -ketophosphonate esters were synthesized. The hydrolytic rates of the compounds under physiological conditions were studied. Most of the compounds are effective inhibitors of acetylcholinesterase. The enzyme recovers on the 10-50 h time scale from its adducts with two of the inhibitors.     

A novel subshape molecular descriptor

Molecules with similar shapes and features often have similar biological activity. Several computational approaches search chemical databases for new leads or templates based on overall molecular shape similarity. However, active molecules often present critical subshapes that are required for binding, which may be missed by comparing overall shape similarity. We present a new approach to compare molecular shapes of different sizes and to calculate subshape similarity. We developed a skeletal representation of the shape which is topologically unrelated to covalent chemical connectivity. This simplifies rotational and translational sampling. We test initial possible alignments by matching similar triangles. This triangle-matching filter rapidly eliminates most geometrically impossible matches. Surviving matches are filtered further in successive stages. These stages involve direction, feature, and shape matching procedures. Our approach is applied to several situations demonstrating lead discovery and evolution.