Organic & Biomolecular Chemistry (v.10, #6)

Front cover (1125-1125).

Inside front cover (1126-1126).

Contents list (1127-1136).

Synthesis of glycosylated 5-hydroxylysine, an important amino acid present in collagen-like proteins such as adiponectin by Katherine R. Herbert; Geoffrey M. Williams; Garth J. S. Cooper; Margaret A. Brimble (1137-1144).
The synthesis of naturally occurring glycosylated (2S,5R)-hydroxylysine still remains a challenge. This perspective highlights the importance of this post-translationally modified amino acid residue in the observed bioactivity of collagen and related collagen-like proteins such as adiponectin, an important target for the treatment of type II diabetes. Strategies employed to date for the syntheses of (2S,5R)-hydroxylysine and the methods to effect glycosylation of this modified amino acid are also summarized herein.

Synthesis and properties of monofluorinated dimyristoylphosphatidylcholine derivatives: Potential fluorinated probes for the study of membrane topology by Jonathan Guimond-Tremblay; Marie-Claude Gagnon; Jozy-Ann Pineault-Maltais; Vanessa Turcotte; Michèle Auger; Jean-François Paquin (1145-1148).
The synthesis of three monofluorinated dimyristoylphosphatidylcholine derivatives (F-DMPC), with the fluorine atom located on the acyl chain in position 2 of the glycerol (sn-2) is described. The synthetic strategy relies on the coupling of 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-PC) and three different fluorinated fatty acids. The latter were obtained from two different and complementary synthetic routes. Preliminary FTIR studies suggest that the presence of the fluorine atom does not significantly perturb the lipid conformational order and phase transition temperature and that these monofluorinated PC derivatives could be used as probes for the study of membrane topology, i.e. the location of drugs, peptides or proteins in membranes.

Cellular uptake of an α-AApeptide by Ge Bai; Shruti Padhee; Youhong Niu; Rongsheng E. Wang; Qiao Qiao; Robert Buzzeo; Chuanhai Cao; Jianfeng Cai (1149-1153).
Some short and cationic peptides such as the Tat peptide can cross the cell membrane and function as vectors for intracellular delivery. Here we show that an α-AApeptide is able to penetrate the membranes of living cells from an extracellular environment and enter the endosome and cytoplasm of cells. The efficiency of the cellular uptake is comparable to a Tat peptide (48–57) of the same length and is unexpectedly superior to an α-peptide with identical functional groups. The mechanism of uptake is similar to that of the Tat peptide and is through endocytosis by an energy-dependent pathway. Due to the easy synthesis of the α-AApeptides, their resistance to proteolytic hydrolysis, and their low cytotoxicity, α-AApeptides represent a new class of transporters for the delivery of drugs.

Towards dual photodynamic and antiangiogenic agents: design and synthesis of a phthalocyanine-chalcone conjugate by Sinem Tuncel; Jérémie Fournier-dit-Chabert; Florian Albrieux; Vefa Ahsen; Sylvie Ducki; Fabienne Dumoulin (1154-1157).
A phthalocyanine–chalcone conjugate has been designed to combine the vascular disrupting effect of chalcones with the photodynamic effect of phthalocyanines. This potential dual photodynamic and antiangiogenic agent was obtained by the condensation of a tetrahydroxylated non-peripherally substituted Zn(ii) phthalocyanine with an amino chalcone converted into the corresponding activated isocyanate. The conjugate was fully characterized.

Direct amination of α-substituted nitroacetates using di-tert-butyl azodicarboxylate catalyzed by Hatakeyama's catalyst β-ICD by Cong-Bin Ji; Yun-Lin Liu; Xiao-Li Zhao; Yin-Long Guo; Hao-Yang Wang; Jian Zhou (1158-1161).
We report the first example of catalytic asymmetric direct amination of α-monosubstituted nitroacetates using di-tert-butyl azodicarboxylate. The simple and easily available Hatakeyama's catalyst β-ICD 11 was found to be a highly enantioselective catalyst for this reaction.

A series of four spiropyrans bearing different substituents on the indolic nitrogen were synthesized and their capability of binding mono and bivalent transition metal cations in solution was assessed via UV-visible absorption spectroscopy. All the compounds responded selectively to the presence of Cu(ii) ions producing intense absorption bands in the visible region of their spectra. Bidimensional 1H-NMR and MALDI-TOF MS spectroscopies revealed the formation of SP dimers mediated by Cu(ii). This is the first example of cross-coupling mediated by copper(ii) in mild conditions causing the symmetric dimerization of spiropyran dyes.

Synthesis, structural investigation and computational modelling of water-binding aquafoldamers by Huaiqing Zhao; Wei Qiang Ong; Xiao Fang; Feng Zhou; Meng Ni Hii; Sam Fong Yau Li; Haibin Su; Huaqiang Zeng (1172-1180).
Detailed studies on water-binding aquafoldamers are presented that illustrate the potential use of the elongated larger aquafoldamers for recognizing larger water clusters of diverse topologies. A novel self-trapping dimerization mode involving two tetramer molecules is proposed, which is consistent with the obtained varying experimental evidences.

Bis-amidocarbazolyl urea receptor for short-chain dicarboxylate anions by M. Belén Jiménez; Victoria Alcázar; Rafael Peláez; Francisca Sanz; Ángel L. Fuentes de Arriba; M. Cruz Caballero (1181-1185).
Urea receptor 1 based on two (1-amino-8-amido-3,6-dichloro)carbazole units shows a strong association with dicarboxylate anions such as oxalate, malonate and succinate guests through multiple hydrogen bonds from the carbazole, urea and amide NH groups. 1H NMR complexation studies exhibit high values of association constants in DMSO-d6. X-ray structures of the 1 : 1 complexes of 1 with oxalate and malonate as their ditetrabutylammonium salts were obtained. A modelling study of the complex of receptor 1 with succinate (as its diTBA salt) showed a more reduced geometric complementarity than its homologue malonate.

A general procedure for the synthesis of alkyl- and arylethynyl-1,2,3-triazole-fused dihydroisoquinolines by Vito Fiandanese; Silvia Maurantonio; Angela Punzi; Giacomo G. Rafaschieri (1186-1195).
A general procedure for the synthesis of the title compounds has been devised starting from the available 2-halophenylethyl azides, by means of click reactions with trimethylsilylacetylene or 1-trimethylsilyl-1,3-butadiyne followed by a transition metal-catalyzed functionalization of C–H bond. A further extension of this procedure led us to devise the synthesis of more complex 4,4′-bitriazole-fused dihydroisoquinolines.

Computational study of radicals derived from hydroxyurea and its methylated analogues by Ivana Vinković Vrček; Davor Šakić; Valerije Vrček; Hendrik Zipse; Mladen Biruš (1196-1206).
Structural and electronic properties and chemical fate of free radicals generated from hydroxyurea (HU) and its methylated analogues N-methylhydroxyurea (NMHU) and O-methylhydroxyurea (OMHU) are of utmost importance for their biological and pharmacological effects. In this work the cis/trans conformational processes, tautomerizations, and intramolecular hydrogen and methyl migrations in hydroxyurea-derived radicals have been considered. Potential energy profiles for these reactions have been calculated using two DFT functionals (BP86 and B3LYP) and two composite models (G3(MP2)RAD and G3B3). Solvation effects have been included both implicitly (CPCM) and explicitly. It has been shown that calculated energy barriers for free radical rearrangements are significantly reduced when a single water molecule is included in calculations. In the case of HU-derived open-shell species, a number of oxygen-, nitrogen-, and carbon-centered radicals have been located, but only the O-centered radicals (e1 and z1) fit to experimental isomeric hyperfine coupling constants (hfccs) from EPR spectra. The reduction of NMHU and OMHU produces O-centered and N-centered radicals, respectively, with the former being more stable by ca. 60 kJ mol−1. The NMHU-derived radical e4 undergoes rearrangements, which can result in formation of several conceivable products. The calculated hfccs have been successfully used to interpret the experimental EPR spectra of the most probable rearranged product 10. Reduction potentials of hydroxyureas, radical stabilization energy (RSE) and bond disocciation energy (BDE) values have been calculated to compare stabilities and reactivities of different subclasses of free radicals. It has been concluded, in agreement with experiment, that reductions of biologically relevant tyrosyl radicals by HU and NMHU are thermochemically favorable processes, and that the order of reactivity of hydroxyureas follows the experimentally observed trend NMHU > HU > OMHU.

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations by Jon I. Mujika; Xabier Lopez; Adrian J. Mulholland (1207-1218).
Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction necessary for this cyclization. Experiments demonstrate that two histidines (the penultimate amino acid of the intein, and a histidine located 10 amino acids upstream) are relevant in the cyclization of the asparagine. We have investigated the mechanism and determinants of reaction in the GyrA intein focusing on the requirements for asparagine activation for its cyclization. First, the influence that the protonation states of these two histidines have on the orientation of the asparagine side chain is investigated by means of molecular dynamics simulation. Molecular dynamics simulations using the CHARMM27 force field were carried out on the three possible protonation states for each of these two histidines. The results indicate that the only protonation state in which the conformation of the system is suitable for cyclization is when the penultimate histidine is fully protonated (positively charged), and the upstream histidine is in the Hisε neutral tautomeric form. The free energy profile for the reaction in which the asparagine is activated by a proton transfer to the upstream histidine is presented, computed by hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics at the SCCDFTB/CHARMM27 level of theory. The calculated free energy barrier for the reaction is 19.0 kcal mol−1. B3LYP/6-31+G(d) QM/MM single-point calculations give a qualitatively a similar energy profile, although with somewhat higher energy barriers, in good agreement with the value derived from experiment of 25 kcal mol−1 at 60 °C. QM/MM molecular dynamics simulations of the reactant, activated reactant and intermediate states highlight the importance of the Arg181-Val182-Asp183 segment in catalysing the reaction. Overall, the results indicate that nucleophilic activation of the asparagine for its cyclization by the upstream histidine acting as the base is a plausible mechanism for the C-terminal cleavage in protein splicing.

Regiodivergent synthesis of trisubstituted furans through Tf2O-catalyzed Friedel–Crafts acylation: a tool for access to tetrahydrofuran lignan analogues by Daniela Comegna; Marina DellaGreca; M. Rosaria Iesce; Lucio Previtera; Armando Zarrelli; Simona Zuppolini (1219-1224).
3- or 4-Aroylfurans have been prepared selectively and in high yields from a common precursor by simple tuning of reaction conditions in Friedel–Crafts acylation promoted by triflic anhydride. The formation of products can be explained on the basis of the ring-chain tautomerism occurring in compounds equipped with two neighbouring carboxylic functions. Since 4-aroylfuran derivatives show a typical lignan backbone, suitable hydrogenation conditions were found out to gain tetrahydrofuran lignans.

Practical synthesis of β-oxo benzo[d]thiazolyl sulfones: Scope and limitations by Jiří Pospíšil; Raphaël Robiette; Hitoshi Sato; Kevin Debrus (1225-1234).
In this paper, we discuss our new synthetic approach towards functionalized benzo[d]thiazolyl (BT) sulfones, based on the reunion of alkyl BT sulfones and various electrophiles (e.g. R–CO–X, RO–CO–X, RS–CO–X, Ts–X…). All important aspects of this coupling reaction, including relevant and undesirable side reactions, are evaluated by means of calculations and competitive experiments. The scope and limitations of this method are established.

Pd-Catalyzed asymmetric hydrogenation of 3-(toluenesulfonamidoalkyl)indoles by Ying Duan; Mu-Wang Chen; Qing-An Chen; Chang-Bin Yu; Yong-Gui Zhou (1235-1238).
A series of 2-substituted 3-(toluenesulfonamidoalkyl)indoles was synthesized by application of (EtO)2POH or iodine as the catalyst, and was hydrogenated using chiral Pd catalyst, giving the 2,3-disubstituted indolines with up to 97% ee.

An efficient and easy procedure to synthesize the pyridinyl analogues of dibenzylideneacetone (pyr-dba) was developed by the condensation of substituted nicotinaldehyde and acetone in the presence of K2CO3 in toluene-EtOH-H2O solvent system. Structurally diverse pyr-dba, including quinolinyl dba, can be prepared conveniently in moderate to excellent yields under mild conditions with this method. The resulting pyr-dba functioned as the enone analogs of curcumin and efficiently inhibited the activation of NF-κB and the growth of colorectal carcinoma HCT116 p53+/+ cells as well as the HIV-1 IN-LEDGF/p75 interaction.

Herein we report the total syntheses of pseudoceramine A-D (2–5) and spermatinamine (1) isolated from the marine sponge Pseudoceratina sp. Direct acyl substitution of α-hydroxyiminoesters with amine nucleophiles was developed as a key transformation. The synthetic compounds confirm the reported structures and importantly gives access to non-symmetrical spermine based natural products carrying two different bromotyrosine building blocks. Our new synthesis of spermatinamine is two steps shorter and more efficient than the previously reported sequence.

A highly diastereoselective Ugi reaction involving a chiral cyclic imine, two enantiomerically pure isocyanides and various carboxylic acids was employed for the synthesis of polyfunctionalized pyrrolidines. Both chiral substrates have been efficiently prepared by chemoenzymatic methodologies from readily available achiral substrates. This highly convergent approach can find an application in the fragment-based drug discovery process.

The one-pot reductive coupling of N-acylcarbamates with activated alkenes is described. The method is based on partial reduction of N-acylcarbamates with DIBAL-H, followed by N-acyliminium ion formation and SmI2-mediated radical coupling with activated alkenes. Both acyclic and cyclic N-acylcarbamates can be used as stable substrates, and a range of activated alkenes serve as effective radical receptors. The reductive coupling of l-N-acylcarbamates 12/13 gave 2,5-disubstituted pyrrolidine derivatives in high trans-diastereoselectivities. The reductive coupling with penta-2,4-dienoate proceeded exclusively in a 1,6-addition fashion, producing a single non-conjugated E-isomer. On the basis of this method, a three-step construction of pyrrolo[1,2-a]azepin-5-one 16, the skeleton of many stemona alkaloids and lehmizidine alkaloids, and a seven-step synthesis of (−)-xenovenine (pyrrolizidine cis-223H, ent-6), the unnatural enantiomer of the frog/ant venom alkaloid possessing potent inhibitory activity towards nAChR channel, were achieved starting from l-12.

Trichogin GA IV: A versatile template for the synthesis of novel peptaibiotics by Marta De Zotti; Barbara Biondi; Cristina Peggion; Fernando Formaggio; Yoonkyung Park; Kyung-Soo Hahm; Claudio Toniolo (1285-1299).
Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 310-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 310- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.

1,4-Diazabicyclo[2.2.2]octane (DABCO) has been evaluated as a starting material for the synthesis of 1-alkyl-4-(2-phenoxyethyl)piperazines and related derivatives. We found that 1-alkyl-1,4-diazabicyclo[2.2.2]octan-1-ium salts, resulting from the alkylation of DABCO, efficiently react with a variety of nucleophiles in polyethyleneglycol (PEG) or diglyme at high temperatures to give piperazine products resulting from the nucleophilic ring-opening reaction. The benzylation side reaction was found to be relevant with softer nucleophiles when using 1-benzyl-1,4-diazabicyclo[2.2.2]octan-1-ium salts, while other types of alkylations were not observed. One-pot methodologies allow for the synthesis of piperazines directly from primary alcohols, alkyl halides or sulfonates, using phenols, or other nucleophile sources, and DABCO.

Back cover (1311-1312).