Impact of azaproline on Peptide conformation

The amino acid analog azaproline (azPro) contains a nitrogen atom in place of the C(alpha) of proline. Peptides containing azPro were shown to stabilize the cis-amide conformer for the acyl-azPro bond and prefer type VI beta-turns both in crystals and in organic solvents by NMR. The increased stability for cis-amide conformers was relatively minor with respect to the trans-conformers. Further, their conformational preferences were depended on solvent. To elucidate the impact of azPro substitution on amide cis-trans isomerism and peptide conformation, this paper reports ab initio studies on azPro derivatives and a comparison with their cognate Pro derivatives: 1-acetyl-2-methyl pyrrolidine (1), 1-acetyl-2-methyl pyrazolidine (2), Ac-Pro-NHMe (3), Ac-azPro-NHMe (4), Ac-azPro-NMe(2) (5), Ac-azAzc-NHMe (6), and Ac-azPip-NHMe (7). Conformational preferences were explored at the MP2/6-31+G** level of theory in vacuo. Solvation effects for 1 and 2 were studied implicitly using the polarizable continuum model and explicitly represented by interactions with a single water molecule. An increase in the conformational preference for the cis-amide conformer of azPro was clearly seen. An intramolecular hydrogen bond occurred solely in the trans-amide conformer that reduced the preference for the cis-conformer by 2.2 kcal/mol. The larger ring homolog aza-pipecolic acid (azPip), in which this internal hydrogen bond was diminished, significantly augmented stabilization of the cis-amide conformer. In aqueous solution, the preference for the cis-amide conformers was greatly reduced, mainly as a result of interaction between water and the lone pair of the alpha-nitrogen in the trans-amide conformer that was 3.8 kcal/mol greater than that in the cis-conformer. In the azPro analog, the energy barrier for cis-trans amide isomerization was 6 kcal/mol less than that in the cognate Pro derivative. Because the azPro derivatives can stabilize the cis-amide bond and mimic a type VI beta-turn without incorporation of additional steric bulk, such a simple chemical modification of the peptide backbone provides a useful conformational constraint when incorporated into the structure of selected bioactive peptides. Such modifications can scan receptors for biological recognition of reverse turns containing cis-amide bonds by the incorporation of type VI beta-turn scaffolds with oriented appended side chains.     

Activity concentrations of 210Po in the soft parts of cockle (Anadara granosa)at Kuala Selangor, Malaysia

Polonium-210 has been measured in the soft parts of Anadara granosa purchased at Kuala Selangor, West Coast of Malaysia in August 2001, April 2002 and September 2002. It is shown that ²¹⁰Po is non-uniformly distributed within cockles of various sizes (i.e., 2.5, 3.0, 3.5 and 4.0 cm of shell length) and the concentration of ²¹⁰Po in the soft parts of cockle was significantly different (p<0.05) due to sampling date. The highest value was observed in the smallest cockle with a shell length of 2.5 cm (411.6±26.16 Bq/g dry wt.). It is clear that there is an allometric relationship between ²¹⁰Po activity concentration and individual cockle weight. This may reflect on the differences of metabolic rate and growth age of cockles. The mean activity concentration of ²¹⁰Po measured in Kuala Selangor filtered water were 1.75±0.17, 0.79±0.08 and 1.13±0.20 Bq/kg for August 2001, April 2002 and September 2002, respectively. The yield concentration factors for ²¹⁰Po in the soft parts of cockles varies from 27.3^. 10³ to 106.9^. 10³. This revised version was published online in July 2006 with corrections to the Cover Date.     

Bruceines K and L from the Ripe Fruits of Brucea javanica

Bruceine K ( 1 ), a pentacyclic C₂₀‐quassinoid bearing a unique 12,20‐epoxy moiety, and bruceine L ( 2 ), along with the ten known compounds (6S,7E)‐6,9,10‐trihydroxy‐ and (6S,7E)‐6,9‐dihydroxymegastigma‐4,7‐dien‐3‐one ( 3 and 4 , resp.), cleomiscosins A–C, luteoline, quercetine, bruceantinol, pinoresinol, and thevetiaflavone, were isolated from the ripe fruits of Brucea javanica. Bruceines K ( 1 ) and L ( 2 ) were determined to be (1β,2α,11β,12β,14ξ,15β)‐12,20‐epoxy‐1,2,11,13,14,15‐hexahydroxypicras‐3‐en‐16‐one and (1β,2α,11β,12β,15β)‐13,20‐epoxy‐1,2,11,12‐tetrahydroxy‐16‐oxo‐15‐(senecioyloxy)picras‐3‐en‐21‐oic acid methyl ester (senecioic acid=3‐methylbut‐2‐enoic acid), respectively, on the basis of NMR (¹H‐ and ¹³C‐NMR, DEPT, ¹H,¹H‐COSY, NOESY, HMQC, and HMBC) and ESI‐MS data. Among the known compounds, (6S,7E)‐6,9,10‐trihydroxy‐ and (6S,7E)‐6,9‐dihydroxymegastigma‐4,7‐dien‐3‐one ( 3 and 4 , resp.), cleomiscosin C, luteoline, quercetine, and thevetiaflavone were isolated for the first time from the Brucea plants.     

Gold(I)‐Catalyzed Enantioselective Intermolecular Hydroarylation of Allenes with Indoles and Reaction Mechanism by Density Functional Theory Calculations

Chiral binuclear gold(I) phosphine complexes catalyze enantioselective intermolecular hydroarylation of allenes with indoles in high product yields (up to 90 %) and with moderate enantioselectivities (up to 63 % ee). Among the gold(I) complexes examined, better ee values were obtained with binuclear gold(I) complexes, which displayed intramolecular Au^I Au^I interactions. The binuclear gold(I) complex 4c [(AuCl)₂( L3 )] with chiral biaryl phosphine ligand (S)‐(−)‐MeO‐biphep ( L3 ) is the most efficient catalyst and gives the best ee value of up to 63 %. Substituents on the allene reactants have a slight effect on the enantioselectivity of the reaction. Electron‐withdrawing groups on the indole substrates decrease the enantioselectivity of the reaction. The relative reaction rates of the hydroarylation of 4‐X‐substituted 1,3‐diarylallenes with N‐methylindole in the presence of catalyst 4c [(AuCl)₂( L3 )] / AgOTf [ L3 =(S)‐(−)‐MeO‐biphep], determined through competition experiments, correlate (r²=0.996) with the substituent constants σ. The slope value is −2.30, revealing both the build‐up of positive charge at the allene and electrophilic nature of the reactive Au^I species. Two plausible reaction pathways were investigated by density functional theory calculations, one pathway involving intermolecular nucleophilic addition of free indole to aurated allene intermediate and another pathway involving intramolecular nucleophilic addition of aurated indole to allene via diaurated intermediate E2 . Calculated results revealed that the reaction likely proceeds via the first pathway with a lower activation energy. The role of Au^I Au^I interactions in affecting the enantioselectivity is discussed.     

A ruler for determining the position of proteins in membranes

Both the oxygen diffusion rate and the oxygen solubility vary with depth into the interior of biological membranes. The product of these two gradients generates a single gradient, a permeability gradient, which is a smooth continuous function of the distance from the center of the membrane. Using electron paramagnetic resonance and the spin-probe method, the relaxation gradient of oxygen, which is directly proportional to the permeability gradient, is the quantity that can be directly measured in membranes under physiological conditions. The gradient obtained provides a calibrated ruler for determining the membrane depth of residues either from loop regions of membrane-binding proteins or from the membrane-exposed residues of transmembrane proteins. We have determined the relaxation gradient of oxygen in zwitterionic and anionic phospholipid membranes by attaching a single nitroxide probe to a transmembrane alpha-helical polypeptide at specific residues. The peptide ruler was used to determine the depth of penetration of the calcium-binding loops of the C2 domain of cytosolic phospholipase A(2). The positions of selected residues of this membrane-binding protein that penetrate into the membrane, determined using this ruler, compared favorably with previous determinations using more complex methods. The relaxation gradient constrains the possible values of the membrane-dependent oxygen concentration and the oxygen diffusion gradients. The average oxygen diffusion coefficient is estimated to be at least 2-fold smaller in the membrane than that in water.     

Stable Anticancer Gold(III)–Porphyrin Complexes: Effects of Porphyrin Structure

In the design of physiologically stable anticancer gold(III) complexes, we have employed strongly chelating porphyrinato ligands to stabilize a gold(III) ion [Chem. Commun. 2003 , 1718; Coord. Chem. Rev. 2009 , 253, 1682]. In this work, a family of gold(III) tetraarylporphyrins with porphyrinato ligands containing different peripheral substituents on the meso‐aryl rings were prepared, and these complexes were used to study the structure–bioactivity relationship. The cytotoxic IC₅₀ values of [Au(Por)]⁺ (Por=porphyrinato ligand), which range from 0.033 to >100 μM , correlate with their lipophilicity and cellular uptake. Some of them induce apoptosis and display preferential cytotoxicity toward cancer cells than to normal noncancerous cells. A new gold(III)–porphyrin with saccharide conjugation [Au(4‐glucosyl‐TPP)]Cl ( 2 a ; H₂(4‐glucosyl‐TPP)=meso‐tetrakis(4‐β‐D ‐glucosylphenyl)porphyrin) exhibits significant cytostatic activity to cancer cells (IC₅₀=1.2–9.0 μM ) without causing cell death and is much less toxic to lung fibroblast cells (IC₅₀>100 μM ). The gold(III)–porphyrin complexes induce S‐phase cell‐cycle arrest of cancer cells as indicated by flow cytometric analysis, suggesting that the anticancer activity may be, in part, due to termination of DNA replication. The gold(III)–porphyrin complexes can bind to DNA in vitro with binding constants in the range of 4.9×10⁵ to 4.1×10⁶ dm³ mol^?1 as determined by absorption titration. Complexes 2 a and [Au(TMPyP)]Cl₅ ( 4 a ; [H₂TMPyP]⁴⁺=meso‐tetrakis(N‐methylpyridinium‐4‐yl)porphyrin) interact with DNA in a manner similar to the DNA intercalator ethidium bromide as revealed by gel mobility shift assays and viscosity measurements. Both of them also inhibited the topoisomerase I induced relaxation of supercoiled DNA. Complex 4 a , a gold(III) derivative of the known G‐quadruplex‐interactive porphyrin [H₂TMPyP]⁴⁺, can similarly inhibit the amplification of a DNA substrate containing G‐quadruplex structures in a polymerase chain reaction stop assay. In contrast to these reported complexes, complex 2 a and the parental gold(III)–porphyrin 1 a do not display a significant inhibitory effect (<10 %) on telomerase. Based on the results of protein expression analysis and computational docking experiments, the anti‐apoptotic bcl‐2 protein is a potential target for those gold(III)–porphyrin complexes with apoptosis‐inducing properties. Complex 2 a also displays prominent anti‐angiogenic properties in vitro. Taken together, the enhanced stabilization of the gold(III) ion and the ease of structural modification render porphyrins an attractive ligand system in the development of physiologically stable gold(III) complexes with anticancer and anti‐angiogenic activities.     

Ruthenium‐Catalyzed Alkylation of Indoles with Tertiary Amines by Oxidation of a sp3 C?H Bond and Lewis Acid Catalysis

Ruthenium porphyrins (particularly [Ru(2,6‐Cl₂tpp)CO]; tpp=tetraphenylporphinato) and RuCl₃ can act as oxidation and/or Lewis acid catalysts for direct C‐3 alkylation of indoles, giving the desired products in high yields (up to 82 % based on 60–95 % substrate conversions). These ruthenium compounds catalyze oxidative coupling reactions of a wide variety of anilines and indoles bearing electron‐withdrawing or electron‐donating substituents with high regioselectivity when using tBuOOH as an oxidant, resulting in the alkylation of N‐arylindoles to 3‐{[(N‐aryl‐N‐alkyl)amino]methyl}indoles (yield: up to 82 %, conversion: up to 95 %) and the alkylation of N‐alkyl or N‐H indoles to 3‐[p‐(dialkylamino)benzyl]indoles (yield: up to 73 %, conversion: up to 92 %). A tentative reaction mechanism involving two pathways is proposed: an iminium ion intermediate may be generated by oxidation of an sp³ C? H bond of the alkylated aniline by an oxoruthenium species; this iminium ion could then either be trapped by an N‐arylindole (pathway A) or converted to formaldehyde, allowing a subsequent three‐component coupling reaction of the in situ generated formaldehyde with an N‐alkylindole and an aniline in the presence of a Lewis acid catalyst (pathway B). The results of deuterium‐labeling experiments are consistent with the alkylation of N‐alkylindoles via pathway B. The relative reaction rates of [Ru(2,6‐Cl₂tpp)CO]‐catalyzed oxidative coupling reactions of 4‐X‐substituted N,N‐dimethylanilines with N‐phenylindole (using tBuOOH as oxidant), determined through competition experiments, correlate linearly with the substituent constants σ (R²=0.989), giving a ρ value of ?1.09. This ρ value and the magnitudes of the intra‐ and intermolecular deuterium isotope effects (k_H/k_D) suggest that electron transfer most likely occurs during the initial stage of the oxidation of 4‐X‐substituted N,N‐dimethylanilines. Ruthenium‐catalyzed three‐component reaction of N‐alkyl/N‐H indoles, paraformaldehyde, and anilines gave 3‐[p‐(dialkylamino)benzyl]indoles in up to 82 % yield (conversion: up to 95 %).     

Theoretical study of mechanism of cycloaddition reaction between dimethylmethylene carbene and formaldehyde

The cycloaddition mechanism of forming a polycyclic compound between singlet dimethylmethylene carbene(R1) and formaldehyde(R2) has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated with CCSD(T)//MP2/6‐31G* method. From the potential energy profile, it can be predicted that the dominant reaction pathway of the cycloadditional reaction between singlet dimethylmethylene carbene and formaldehyde consists of two steps: (1) the two reactants(R1, R2) firstly form an energy‐enricheded intermediate (INT1a) through a barrier‐free exothermic reaction of ΔE = 11.3 kJ/mol. (2) Intermediate (INT1a) then isomerizes to a three‐membered product (P1) via a transition state (TS1a) with an energy barrier of 20.0 kJ/mol. The dominant reaction has an excellent selectivity and differs considerably from its competitive reactions in reaction rate. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Coordination networks from Cu cations and tetrakis(methylthio)benzenedicarboxylic acid: tunable bonding patterns and selective sensing for NH(3) gas

This paper aims to illustrate the rich potential of the thioether-carboxyl combination in generating coordination networks with tunable and interesting structural features. By simply varying the ratio between Cu(NO(3))(2) and the bifunctional ligand tetrakis(methylthio)benzenedicarboxylic acid (TMBD) as the reactants, three coordination networks can be hydrothermally synthesized in substantial yields, which present a distinct evolution with regard to metal-ligand interactions. Specifically, Cu(TMBD)(0.5)(H(2)TMBD)(0.5)·H(2)TMBD (1) was obtained with a relatively small (1:1) Cu(NO(3))(2)/TMBD ratio, and crystallizes as an one-dimensional (1D) coordination assembly based on Cu(I)-thioether interactions, which is integrated by hydrogen-bonding to additional H(2)TMBD molecules to form a three-dimensional (3D) composite network with all the carboxylic acid and carboxylate groups remaining uncoordinated to the metal ions. A medium (1.25:1) Cu(NO(3))(2)/TMBD ratio leads to compound Cu(2)TMBD, in which Cu(I) ions simultaneously bond to the carboxylate and thioether groups, while an even higher (2.4:1) Cu(NO(3))(2)/TMBD ratio produced a mixed-cation compound Cu(II)(2)OHCu(I)(TMBD)(2)·2H(2)O (2), in which the carboxylic groups are bonded to (cupric) Cu(II) ions, and the thioether groups to Cu(I). Despite the lack of open channels in 2, crystallites of this compound exhibit a distinct and selective absorption of NH(3), with a concomitant color change from green to blue, indicating substantial network flexibility and dynamics with regards to gas transport.