Organic & Biomolecular Chemistry (v.10, #36)

Front cover (7229-7229).

Inside front cover (7230-7230).

Contents list (7231-7240).

Traditionally, the biological fluorination of complex biological systems like proteins is achieved through substitution of canonical amino acids or addition of fluorinated amino acids in the context of the standard genetic code. Ribosomal translation of monofluorinated amino acids into proteins often yields structures with minimal local changes in the interior but, on the same time, results in large global effects on characteristic features of the biopolymers (such as dramatically changed activity profile or folding stability). This is due to the novel and unique local interactions delivered by fluorine atoms such as (i) increase in the covalent radii (ii) changed polarities; (iii) changed hydrogen bond acceptor ability; (iv) altered water solubility as well as water ↔ organic solvent energy transfer. On the other hand, the biological incorporation of tri- or global fluorinated amino acids (such as trifluoroleucine, triflurovaline, and their hexafluoro counterparts, fluoromethionine and trifluoronorleucine etc.) represents still a challenge, as the natural structural scaffolds are optimized for hydrocarbon during evolution but not for fluorocarbon cores. Future work will be focused on the re-design of existing or de novo design of novel protein scaffolds capable of accommodating such building blocks into functional biologically active proteins and proteomes in the context of the viable cells.

From biomass to medicines. A simple synthesis of indolo[3,2-c]quinolines, antimalarial alkaloid isocryptolepine, and its derivatives by Maxim G. Uchuskin; Arkady S. Pilipenko; Olga V. Serdyuk; Igor V. Trushkov; Alexander V. Butin (7262-7265).
Indolo[3,2-c]quinolines are pharmacologically attractive class of heterocyclic compounds. The method of their synthesis, based on transformation of furfural, which is a large-scale product of treatment of biomass including agricultural and forestry wastes, has been developed. This method was utilized for the total synthesis of antimalarial alkaloid isocryptolepine and its derivatives.

An efficient and practical copper-catalyzed highly regio- and stereoselective borylcupration of internal alkynes with bis(pinacolato)diboron using a catalytic amount of K2CO3 as base producing Z-alkenylboron compounds has been demonstrated by applying the ligand effect: commercially available electron-rich tris(p-methoxyphenyl) phosphine ensures a smooth and efficient reaction. Functionalized alkynes, such as propargylic alcohols and derivatives as well as N-propargyl tosylamide, may also be used with excellent selectivity.

Unprecedented Ullmann couplings of murrayafoline-A with either 6-bromo- or 4-bromocarbazole derivatives provide highly efficient synthetic routes to the biscarbazole alkaloids murrastifoline-A (6 steps, 66% overall yield) and bismurrayafoline-A (6 steps, 28% overall yield).

Palladium-catalyzed atom transfer radical cyclization of unactivated alkyl iodide by Hui Liu; Zongjun Qiao; Xuefeng Jiang (7274-7277).
A palladium-catalyzed atom transfer cyclization of unactivated alkyl iodide has been developed. A radical chain mechanism has been proposed for this transformation, which might not involve an alkylpalladium intermediate.

Pyridoxine reaction with 1O2 in aqueous solution at neutral pH resulted in oxidation at the 2- and 6-positions of the pyridine ring and unprecedented ring contraction. Kinetic and low temperature studies provided observable intermediates by NMR spectroscopy. In addition, novel cycloaddition between pyridoxine and N-methylmaleimide, without N-alkylation and in water, suggest a common [3 + 2] cycloaddition with the 3-hydroxypyridine ring.

The effect of varying the size of the macrocycle component on the formation of anion templated imidazolium interpenetrated assemblies is investigated. Two different approaches to reducing the macrocycle size are undertaken and the stabilities of the resulting pseudorotaxanes incorporating substituted imidazolium threading components studied using 1H NMR spectroscopy. Novel imidazolium axle containing interlocked rotaxane host structures are synthesised using chloride anion templated amide condensation and ‘stoppering’ methods, and the anion recognition properties of the ‘stoppered’ rotaxane investigated.

Toluene dioxygenase-catalyzed cis-dihydroxylation of benzo[b]thiophenes and benzo[b]furans: synthesis of benzo[b]thiophene 2,3-oxide by Derek R. Boyd; Narain D. Sharma; Ian N. Brannigan; Timothy A. Evans; Simon A. Haughey; Brian T. McMurray; John F. Malone; Peter B. A. McIntyre; Paul J. Stevenson; Christopher C. R. Allen (7292-7304).
Enzymatic cis-dihydroxylation of benzo[b]thiophene, benzo[b]furan and several methyl substituted derivatives was found to occur in both the carbocyclic and heterocyclic rings. Relative and absolute configurations and enantiopurities of the resulting dihydrodiols were determined. Hydrogenation of the alkene bond in carbocyclic cis-dihydrodiols and ring-opening epimerization/reduction reactions of heterocyclic cis/trans-dihydrodiols were also studied. The relatively stable heterocyclic dihydrodiols of benzo[b]thiophene and benzo[b]furan showed a strong preference for the trans configuration in aqueous solutions. The 2,3-dihydrodiol metabolite of benzo[b]thiophene was utilized as a precursor in the chemoenzymatic synthesis of the unstable arene oxide, benzo[b]thiophene 2,3-oxide.

The remarkable catalytic effects of Fe(OTf)3 in the context of the Pd(ii)-catalyzed conjugate addition of arylboronic acids to chromones were observed to yield a variety of flavanones under mild conditions. The addition of catalytic amounts of DDQ and KNO2 to the reactions exclusively yielded flavone analogs. The reaction scope for the transformation was fairly broad, affording good yields of a wide range of flavanones and flavones, which are privileged structures in many biologically active compounds.

The first organocatalytic enantioselective direct vinylogous Michael reaction of α,β-unsaturated γ-butyrolactam to nitroolefins is developed using cinchona alkaloids as the catalysts. Both product enantiomers are accessible with moderate to good enantioselectivity.

Selective reduction of ketones using water as a hydrogen source under high hydrostatic pressure by Anna Tomin; Alexander Lazarev; Matthew P. Bere; Hana Redjeb; Béla Török (7321-7326).
A selective reduction of a broad variety of ketones is described. The method is based on the combination of a Ni–Al alloy and high hydrostatic pressure (HHP, 2.8 kbar) in an aqueous medium. The reaction of the Ni–Al alloy with water provides in situ hydrogen generation and the high pressure ensures that the H2 formed remains in the solution, thus the CO reduction readily occurs. The application of the HHP resulted in selective formation of the desired products and the common problem of non-selective overhydrogenation could be avoided. In most cases the reductions resulted in high yields and excellent selectivities without the use of any base.

Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond by Akihiko Hatano; Munehiro Okada; Gota Kawai (7327-7333).
Here, we present the solution structure of a DNA duplex containing a disulfide base pair (S-DNA). The unnatural nucleoside “S” possessing a thiophenyl group as base was incorporated into a self-complementary singled-stranded oligonucleotide. Crosslinking of the disulfide base pair was analyzed by non-denaturing polyacrylamide gel electrophoresis. Under oxidizing conditions a high molecular weight band as 18 mer, corresponding to the double-stranded molecule (5′-GCGASTCGC: 3′-CGCTSAGCG), was found, whereas single-stranded self-complementary 9 mer oligonucleotide GCGASTCGC was detected in the presence of a reducing agent. These results suggest that the oligonucleotide is covalently linked by disulfide bonding under oxidizing conditions, which can be reversibly reduced to two thiol groups under reducing conditions. CD spectrum of S-DNA (CGASTCG) under oxidizing conditions suggested that the duplex had a right-handed double-stranded structure similar to that of natural DNA (B-form, CGATCG). NMR studies confirmed that this CGASTCG resembled natural B-DNA and that the two phenyl rings derived from the disulfide base pairing intercalated into the duplex. However, these two phenyl rings were not positioned in the same plane as the other base pairs. Specifically, NOEs suggest that although CGASTCG adopts a structure similar to B-type DNA, the S-DNA duplex is bent at the point of disulfide base pairing to face the major groove.

Towards β-selectivity in functional estrogen receptor antagonists by Jose Juan Rodríguez; Kamila Filipiak; Maciej Maslyk; Jakub Ciepielski; Sebastian Demkowicz; Sonia de Pascual-Teresa; Sonsoles Martín-Santamaría; Beatriz de Pascual-Teresa; Ana Ramos (7334-7346).
Based on the benzo[b]naphtho[1,2-d]furan and benzo[b]naphtho[1,2-d]thiophene frameworks, a series of ligands with different basic side chains (BSCs) has been synthesized and pharmacologically evaluated. Also, their binding modes have been modelled using docking techniques. It was found that the introduction of a BSC in these systems brings about a decrease of affinity for both estrogen receptors α and β in an in vitro competitive binding assay. However, two full antagonists of the estrogen receptor β (9c and 9f) have been discovered, with potency in the low micromolar concentration in a cell-based luciferase reporter assay, and completely devoid of activity against the α receptor at the same concentration range. Differences in the ERα/ERβ binding modes have also been rationalized with the help of molecular modelling techniques. This interesting functional profile could be used to elucidate the physiological role of each ER subtype.

Allyltrimethylsilane (allyl-TMS) reacts with propargylic alcohols 1a–1d in the presence of 10% Bi(OTf)3 in [BMIM][BF4] solvent to furnish the corresponding 1,5-enynes in respectable isolated yields (87–93%) at room temperature. The utility of Bi(OTf)3 as a superior catalyst was demonstrated in a survey study on coupling of allyl-TMS with 1a employing several metallic triflates (Bi, Ln, Al, Yb) as well as, B(C6F5)3, Zn(NTf2)2 and Bi(NO3)3·5H2O. Coupling of cyclopropyl substituted propargylic alcohol 1e with allyl-TMS gave the skeletally intact 1,5-enyne and a ring opened derivative as a mixture. Coupling of propargylic/allylic alcohol 1f with allyl-TMS resulted in allylation at both benzylic (2 isomers) and propargylic positions, as major and minor products respectively. The scope of this methodology for allylation of a series of allylic and benzylic alcohols was explored. Chemoselective reduction of a host of propargylic, propagylic/allylic, bis-allylic, allylic, and benzylic alcohols with Et3SiH was achieved in high yields with short reaction times. The same approach was successfully applied to couple representative propargylic and allylic alcohols with 1-phenyl-2-trimethylsilylacetylene. The recovery and reuse of the ionic liquid (IL) was gauged in a case study with minimal decrease in isolated yields after six cycles.

The α-hydroxydepsipeptide 3-carboxyphenyl N-(phenylacetyl)-α-hydroxyglycinate (5) is a quite effective substrate of serine β-lactamases and low molecular mass dd-peptidases. The class C P99 and ampC β-lactamases catalyze the hydrolysis of both enantiomers of 5, although they show a strong preference for one of them. The class A TEM-2 and class D OXA-1 β-lactamases and the Streptomyces R61 and Actinomadura R39 dd-peptidases catalyze hydrolysis of only one enantiomer of 5 at any significant rate. Experiments show that all of the above enzymes strongly prefer the same enantiomer, a surprising result since β-lactamases usually prefer l(S) enantiomers and dd-peptidases d(R). Product analysis, employing peptidylglycine α-amidating lyase, showed that the preferred enantiomer is d(R). Thus, it is the β-lactamases that have switched preference rather than the dd-peptidases. Molecular modeling of the P99 β-lactamase active site suggests that the α-hydroxyl of 5 may interact with conserved Asn and Lys residues. Both α-hydroxy and α-amido substituents on a glycine ester substrate can therefore enhance its productive interaction with the β-lactamase active site, although their effects are not additive; this may also be true for inhibitors.

Fluorescently labeled oligonucleotides are commonly employed as probes to detect specific DNA or RNA sequences in homogeneous solution. Useful probes should experience strong increases in fluorescent emission upon hybridization with the target. We developed dual labeled peptide nucleic acid probes, which signal the presence of complementary DNA or RNA by up to 450-fold enhancements of fluorescence intensity. This enabled the very sensitive detection of a DNA target (40 pM LOD), which was detectable at less than 0.1% of the beacon concentration. In contrast to existing DNA-based molecular beacons, this PNA-based method does not require a stem sequence to enforce dye–dye communication. Rather, the method relies on the energy transfer between a “smart” thiazole orange (TO) nucleotide, which requires formation of the probe–target complex in order to become fluorescent, and terminally appended acceptor dyes. To improve upon fluorescence responsiveness the energy pathways were dissected. Hydrophobic, spectrally mismatched dye combinations allowed significant (99.97%) decreases of background emission in the absence of a target. By contrast, spectral overlap between TO donor emission and acceptor excitation enabled extremely bright FRET signals. This and the large apparent Stokes shift (82 nm) suggests potential applications in the detection of specific RNA targets in biogenic matrices without the need of sample pre-processing prior to detection.

Investigating the oxidation of alkenes by non-heme iron enzyme mimics by Sarah M. Barry; Helge Mueller-Bunz; Peter J. Rutledge (7372-7381).
Iron is emerging as a key player in the search for efficient and environmentally benign methods for the functionalisation of C–H bonds. Non-heme iron enzymes catalyse a diverse array of oxidative chemistry in nature, and small-molecule complexes designed to mimic the non-heme iron active site have great potential as C–H activation catalysts. Herein we report the synthesis of a series of organic ligands that incorporate key features of the non-heme iron active site. Iron(ii) complexes of these ligands have been generated in situ and their ability to promote hydrocarbon oxidation has been investigated. Several of these systems promote the biomimetic dihydroxylation of cyclohexene at low levels, when hydrogen peroxide is used as the oxidant; allylic oxidation products are also observed. An investigation of ligand stability reveals formation of several breakdown products under the conditions of the oxidative turnover reactions. These products arise via oxidative decarboxylation, dehydration and deamination reactions. Taken together these results indicate that competing mechanisms are at play with these systems: biomimetic hydroxylation involving high-valent iron species, and allylic oxidation via Fenton chemistry and Haber–Weiss radical pathways.

Direct participation of counter anion in acid hydrolysis of glycoside by Hung Duy Phan; Tomoya Yokoyama; Yuji Matsumoto (7382-7391).
The mechanism of acid hydrolysis of glycoside has been investigated since the end of the 19th century accompanied by lots of literatures published on the mechanism, although little attention has surprisingly been paid to the action of counter anion of acid. In this paper, it was investigated whether or not counter anion of acid directly participates in acid hydrolysis of glycosides, methyl α- and β-d-glucopyranosides (MGP) in water, aqueous 74%, and 82% 1,4-dioxane systems. Because proton activity of a reaction system is the important rate-determining parameter in the universally acknowledged mechanism, it was carefully estimated in this study. The results suggested that bromide anion directly participates in the acid hydrolysis reaction of MGP in a water solvent system and the participation of bromide anion is further pronounced in aqueous 74% and 82% 1,4-dioxane solvent systems. It was also suggested that chloride anion directly participates in these dioxane solvent systems.

Resorcinarene-based cavitands with chiral amino acid substituents for chiral amine recognition by Na Li; Fan Yang; Hillary A. Stock; David V. Dearden; John D. Lamb; Roger G. Harrison (7392-7401).
Resorcinarene-based deep cavitands alanine methyl resorcinarene acid (AMA), alanine undecyl resorcinarene acid (AUA) and glycine undecyl resorcinarene acid (GUA), which contain chiral amino acids, have been synthesized. The upper rim of the resorcinarene host is elongated with four identical substituents topped with alanine and glycine groups. The structures of the new resorcinarenes were elucidated by nuclear magnetic resonance (NMR), mass spectrometry (MS) and the sustained off-resonance irradiation collision induced dissociation (SORI-CID) technique in FTICR-MS. These studies revealed that eight water molecules associate to the cavitand, two for each alanine group. The alanine substituent groups are proposed to form a kite-like structure around the resorcinarene scaffold. The binding of AMA, AUA, and GUA with chiral R- and S-methyl benzyl amines was studied by 1H NMR titration, and compared to that of a binary l-tartaric acid and the monoacid phthalyl alanine (PA). The results show that these compounds interact with amine guests; however, with four carboxylic acid groups, they bind several amine molecules strongly while the binary l-tartaric acid only binds one amine guest strongly. The simple compound PA, which contains one carboxylic group, shows weak binding to the amines. The 1H NMR titration of AUA with primary, secondary, and tertiary chiral amines showed that it can discriminate between these three types of amines and showed chiral discrimination for chiral secondary amines.

Development of a novel class of B-RafV600E-selective inhibitors through virtual screening and hierarchical hit optimization by Xiangqian Kong; Jie Qin; Zeng Li; Adina Vultur; Linjiang Tong; Enguang Feng; Geena Rajan; Shien Liu; Junyan Lu; Zhongjie Liang; Mingyue Zheng; Weiliang Zhu; Hualiang Jiang; Meenhard Herlyn; Hong Liu; Ronen Marmorstein; Cheng Luo (7402-7417).
Oncogenic mutations in critical nodes of cellular signaling pathways have been associated with tumorigenesis and progression. The B-Raf protein kinase, a key hub in the canonical MAPK signaling cascade, is mutated in a broad range of human cancers and especially in malignant melanoma. The most prevalent B-RafV600E mutant exhibits elevated kinase activity and results in constitutive activation of the MAPK pathway, thus making it a promising drug target for cancer therapy. Herein, we describe the development of novel B-RafV600E selective inhibitors via multi-step virtual screening and hierarchical hit optimization. Nine hit compounds with low micromolar IC50 values were identified as B-RafV600E inhibitors through virtual screening. Subsequent scaffold-based analogue searching and medicinal chemistry efforts significantly improved both the inhibitor potency and oncogene selectivity. In particular, compounds 22f and 22q possess nanomolar IC50 values with selectivity for B-RafV600Ein vitro and exclusive cytotoxicity against B-RafV600E harboring cancer cells.

Synthesis and evaluation of thiosemicarbazones functionalized with furyl moieties as new chemosensors for anion recognition by Luis E. Santos-Figueroa; María E. Moragues; M. Manuela M. Raposo; Rosa M. F. Batista; Susana P. G. Costa; R. Cristina M. Ferreira; Félix Sancenón; Ramón Martínez-Máñez; José Vicente Ros-Lis; Juan Soto (7418-7428).
A family of heterocyclic thiosemicarbazone dyes (3a–f and 4) containing furyl groups was synthesized in good yields, characterized and their response in acetonitrile in the presence of selected anions was studied. Acetonitrile solutions of 3a–f and 4 showed absorption bands in the 335–396 nm range which are modulated by the electron donor or acceptor strength of the heterocyclic systems appended to the thiosemicarbazone moiety. Fluoride, chloride, bromide, iodide, dihydrogen phosphate, hydrogen sulphate, nitrate, acetate and cyanide anions were used in recognition studies. From these anions, only sensing features were seen for fluoride, cyanide, acetate and dihydrogen phosphate. Two clearly different chromo-fluorogenic behaviours were observed: (i) a small shift of the absorption band due to the coordination of the anions with the thiourea protons and (ii) the appearance of a new red shifted band due to deprotonation. For the latter effect, a change in the colour of solution from pale yellow to purple was observed. Fluorescence studies were also in agreement with the different effects observed in the UV/Vis titrations. In this case, hydrogen bonding interactions were visible through the enhancement of the emission band, whereas deprotonation induced the appearance of a new red-shifted emission. Logarithms of stability constants for the two processes (complex formation + deprotonation) for receptors 3a–f in the presence of fluoride and acetate anions were determined from spectrophotometric titrations using the HypSpec V1.1.18 program. Semi-empirical calculations to evaluate the hydrogen-donating ability of the receptors and a prospective electrochemical characterization of compound 3b in the presence of fluoride were also performed.

New multifunctional chiral phosphine (phosphine-amide type) LB8 and BINOL derivative co-catalyzed asymmetric aza-MBH reaction of 5,5-disubstituted cyclopent-2-enones 1 with N-sulfonated imines 2 afforded the corresponding optically active adducts 3 in good to outstanding yields with moderate to good ee's under mild conditions. The steric hindrance environment of BINOL derivatives as well as the nucleophilicity of the phosphorus center and the acidity of free OH which could significantly affect the stereochemical and chemical outcomes had been discussed, indicating the co-catalyzed system is very important to this particular asymmetric aza-MBH reaction.

Back cover (7439-7440).