Organic & Biomolecular Chemistry (v.13, #27)

Front cover (7341-7341).

Inside front cover (7342-7342).

Contents list (7343-7350).

Fluorinated enol ethers: their synthesis and reactivity by M. Decostanzi; J.-M. Campagne; E. Leclerc (7351-7380).
Thanks to the beneficial effect of fluorine substitution on the pharmacokinetic properties of molecules, an ever increasing number of marketed drugs incorporate a fluorine atom into their structure. As a consequence, the synthesis of fluorinated molecules has become a very active research field. Among the numerous approaches, fluorinated enol ethers are valuable building blocks that allow the introduction of a fluoro- or difluoromethyl group through a wide variety of reactions. The present review lists different methods for their preparation and sums up their numerous synthetic applications.

Synthesis of benzimidazoles via iridium-catalyzed acceptorless dehydrogenative coupling by Xiang Sun; Xiao-Hui Lv; Lin-Miao Ye; Yu Hu; Yan-Yan Chen; Xue-Jing Zhang; Ming Yan (7381-7383).
Iridium-catalyzed acceptorless dehydrogenative coupling of tertiary amines and arylamines has been developed. A number of benzimidazoles were prepared in good yields. An iridium-mediated C–H activation mechanism is suggested. This finding represents a novel strategy for the synthesis of benzimidazoles.

Twisted amide electrophiles enable cyclic peptide sequencing by Serge Zaretsky; Vishal Rai; Gerald Gish; Matthew W. Forbes; Michael Kofler; Joy C. Y. Yu; Joanne Tan; Jennifer L. Hickey; Tony Pawson; Andrei K. Yudin (7384-7388).
There is an ever-increasing interest in synthetic methods that not only enable peptide macrocyclization, but also facilitate downstream application of the synthesized molecules. We have found that aziridine amides are stereoelectronically attenuated in a macrocyclic environment such that non-specific interactions with biological nucleophiles are reduced or even shut down. The electrophilic reactivity, revealed at high pH, enables peptide sequencing by mass spectrometry, which will further broaden the utility of aziridine amide-containing libraries of macrocycles.

An unprecedented highly stereoselective example of nickel-catalyzed Suzuki–Miyaura type cross-coupling reactions of (2,2-difluorovinyl)benzene derivatives with arylboronic acids was developed. The reaction proceeded efficiently in the presence of 5 mol% NiCl2(PCy3)2 and K3PO4, affording the Z-fluorostyrene derivatives in good to high yields with excellent regioselectivity.

(R)-VAPOL-Zn(ii) complexes catalysed the enantioselective addition of terminal alkynes to cyclic benzoxathiazine 2,2-dioxides, providing the corresponding chiral propargylic sulfamidates with high yields (up to 93%) and good enantiomeric excesses (up to 87%).

A simple and efficient catalytic system for direct conversion of methylarenes into aromatic oximes has been developed, with Cu(OAc)2 as catalyst, NHPI (N-Hydroxyphthalimide) as additive, TBN (tert-butyl nitrite) as both the nitrogen source and the oxidant. This process proceeds under mild conditions, tolerates a wide range of substrates, affording the targeted aromatic oximes in 63–86% yields.

A model β-sheet interaction and thermodynamic analysis of β-strand mimetics by Colin W. Robinson; Carl S. Rye; Nicola E. A. Chessum; Keith Jones (7402-7407).
β-Sheet mediated protein–protein interactions are involved in key signalling pathways in diseases such as cancer. We present small molecule β-strand mimetics and investigate their interactions with a model tripeptide. Using 1H NMR, the thermodynamic parameters for their binding are determined. These give insight into this biologically important interaction.

Visual detection of formaldehyde by highly selective fluorophore labeling via gold(iii) complex-mediated three-component coupling reaction by Kong-Fan Wong; Jie-Ren Deng; Xiao-Qun Wei; Shi-Ping Shao; Da-Peng Xiang; Man-Kin Wong (7408-7411).
A novel method for visual detection of formaldehyde with excellent selectivity via a gold(iii) complex-mediated three-component coupling reaction of resin-linked sterically bulky amines and fluorescent alkynes has been developed.

A computational study based on density functional theory (DFT) establishes the mechanisms for synergistic Au/Ga catalyzed addition of unactivated terminal alkynes to dicarbonyls, the Nakamura reaction. The role played by each of the metal catalysts and the counterion in the reaction has been elucidated. It has been shown that the triazole (TA) ligand could specifically activate the formation of a particular regioisomer through strong non-covalent interactions. Calculated regioselectivities and activation free energies are in excellent agreement with the experimental results. Observed regioselectivities were rationalized employing a distortion interaction analysis which suggests that the interaction between metal activated reactant fragments in the transition state geometries is a major factor that contributes to the overall barrier height and selectivity. Such enhanced preference for the reaction at the alkyl/aryl substituted carbon of alkynes was strongly influenced by the additional non-covalent interactions exerted by the TA ligand. Excellent agreement between the calculations using a homogeneous gold complex as the catalyst and experimentally observed kinetics and selectivity negates the role of in situ formed gold clusters in the Nakamura reaction.

The oxidative damage to the human telomere: effects of 5-hydroxymethyl-2′-deoxyuridine on telomeric G-quadruplex structures by Antonella Virgilio; Veronica Esposito; Luciano Mayol; Concetta Giancola; Luigi Petraccone; Aldo Galeone (7421-7429).
As part of the genome, human telomeric regions can be damaged by the chemically reactive molecules responsible for oxidative DNA damage. Considering that G-quadruplex structures have been proven to occur in human telomere regions, several studies have been devoted to investigating the effect of oxidation products on the properties of these structures. However only investigations concerning the presence in G-quadruplexes of the main oxidation products of deoxyguanosine and deoxyadenosine have appeared in the literature. Here, we investigated the effects of 5-hydroxymethyl-2′-deoxyuridine (5-hmdU), one of the main oxidation products of T, on the physical–chemical properties of the G-quadruplex structures formed by two human telomeric sequences. Collected calorimetric, circular dichroism and electrophoretic data suggest that, in contrast to most of the results on other damage, the replacement of a T with a 5-hmdU results in only negligible effects on structural stability. Reported results and other data from literature suggest a possible protecting effect of the loop residues on the other parts of the G-quadruplexes.

The study on a fluorescent probe that undergoes a H2S mediated cascade reaction to form an iminocoumarin fluorophore is reported. The probe features better water solubility and fast sensing time (t1/2 = 6.1 min and response time = 24 min) as key advances compared to the reported probe that works on a similar mechanism. The sensing mechanism of the probe was demonstrated by mass spectrometric, HPLC titration and FT-IR titration methods. H2S sensing by the probe was characterized by a 31-fold fluorescence enhancement and alimit of detection of 169 nM. Application of the probe was demonstrated by imaging of H2S in live cells.

Phosphonate derivatives of tetraazamacrocycles as new inhibitors of protein tyrosine phosphatases by Oleksandr L. Kobzar; Michael V. Shevchuk; Alesya N. Lyashenko; Vsevolod Yu. Tanchuk; Vadim D. Romanenko; Sergei M. Kobelev; Alexei D. Averin; Irina P. Beletskaya; Andriy I. Vovk; Valery P. Kukhar (7437-7444).
α,α-Difluoro-β-ketophosphonated derivatives of tetraazamacrocycles were synthesized and found to be potential inhibitors of protein tyrosine phosphatases. N-Substituted conjugates of cyclam and cyclen with bioisosteric phosphonate groups displayed good activities toward T-cell protein tyrosine phosphatase with IC50 values in the micromolar to nanomolar range and showed selectivity over PTP1B, CD45, SHP2, and PTPβ. Kinetic studies indicated that the inhibitors can occupy the region of the active site of TC-PTP. This study demonstrates a new approach which employs tetraazamacrocycles as a molecular platform for designing inhibitors of protein tyrosine phosphatases.

Exploring carbonic anhydrase inhibition with multimeric coumarins displayed on a fullerene scaffold by Marta Abellán-Flos; Muhammet Tanç; Claudiu T. Supuran; Stéphane P. Vincent (7445-7451).
Carbonic anhydrases (CAs) are ubiquitous Zn metallo-enzymes that catalyze the reversible hydration/dehydration of CO2/HCO3. CAs are involved in many key biological processes, therefore their inhibition has become an attractive research field. Distinct families of CA inhibitors (CAIs) have been reported, most of them interacting with the Zn(ii) at the active site. Some compounds such as the coumarins are hydrolyzed before binding the entrance of the active site cavity, and thus behave as “suicide” inhibitors. This study reports the first synthesis of multimeric suicide inhibitors, designed to address the selectivity and the potency of CA multivalent inhibition. Twelve coumarin units have been grafted to a central fullerene scaffold thanks to a CuAAC reaction and the final dodecamers were assayed against 4 relevant CAs. The multimers were always stronger inhibitors than the monomeric species but no strong “multivalent effect” was found. However, our study showed that the multimeric presentation of the coumarin around the C60, indeed affected the selectivity of the relative inhibition among the 4 CAs assayed.

Anti-inflammatory diterpene dimers from the root barks of Aphanamixis grandifolia by Hong-Jian Zhang; Yang-Mei Zhang; Jian-Guang Luo; Jun Luo; Ling-Yi Kong (7452-7458).
A total of 14 new diterpene dimers, aphanamenes C–P (1–14), with four known homologous compounds were isolated from the root barks of Aphanamixis grandifolia Bl. The structures of these compounds were elucidated by spectroscopic analyses, and their absolute configurations were determined using the CD exciton chirality method. In addition, all the compounds exhibited significant inhibition of lipopolysaccharide-induced nitric oxide production in RAW264.7 macrophages, with IC50 values between 7.75 and 38.23 μM.

8-Aza-3,7-dideaza-2′-deoxyadenosine 1 and its C3-naphthylethynylated derivative 3n7zA (2) comprising a 8-aza-3,7-dideazapurine (pyrazolo[4,3-c]pyridine) skeleton were synthesized for the first time. In particular, nucleoside 3n7zA (2) exhibited environmentally sensitive intramolecular charge transfer (ICT) emission because of electron transition in the coplanar conformer formed by nucleobase and naphthalene moieties. Its incorporation into oligodeoxynucleotide (ODN) probes enable a clear identification of a perfectly matched thymine (T) in the complementary strand by a distinct change in the emission wavelength. In addition, the fluorescence emission of the duplexes containing a cytosine/guanine (C/G) base pair flanking 3n7zA (2) was strongly quenched by guanine only when the opposite base of the modified nucleoside was mismatched, enhancing its base identification ability. Thus, ODN probes containing 3n7zA (2) acted as effective reporter probes for homogeneous single nucleotide polymorphism (SNP) typing.

Expanding the scope of N → S acyl transfer in native peptide sequences by Ben Cowper; Leila Shariff; Wenjie Chen; Samantha M. Gibson; Wei-Li Di; Derek Macmillan (7469-7476).
Understanding the factors that influence N → S acyl transfer in native peptide sequences, and discovery of new reagents that facilitate it, will be key to expanding its scope and applicability. Here, through a study of short model peptides in thioester formation and cyclisation reactions, we demonstrate that a wider variety of Xaa-Cys motifs than originally envisaged are capable of undergoing efficient N → S acyl transfer. We present data for the relative rates of thioester formation and cyclisation for a representative set of amino acids, and show how this expanded scope can be applied to the production of the natural protease inhibitor Sunflower Trypsin Inhibitor-1 (SFTI-1).

Evaluation of the antibacterial and antibiofilm activities of novel CRAMP–vancomycin conjugates with diverse linkers by Nigam M. Mishra; Yves Briers; Chris Lamberigts; Hans Steenackers; Stijn Robijns; Bart Landuyt; Jos Vanderleyden; Liliane Schoofs; Rob Lavigne; Walter Luyten; Erik V. Van der Eycken (7477-7486).
We report the design, synthesis and antibacterial activity analysis of conjugates of vancomycin and cathelicidin-related antimicrobial peptides (CRAMP). Vancomycin inhibits the nascent peptidoglycan synthesis and is highly active against Gram-positive bacteria, whereas Gram-negative bacteria are generally insensitive due to a protective outer membrane. CRAMP is known to translocate across the Gram-negative outer membrane by a self-promoted uptake mechanism. Vancomycin–CRAMP conjugates were synthesized using click chemistry with diverse hydrophilic and hydrophobic linkers, with CRAMP functioning as a carrier peptide for the transfer of vancomycin through the outer membrane. Small hydrophobic linkers with an aromatic group result in the most active conjugates against planktonic Gram-negative bacteria, while maintaining the high activity of vancomycin against Gram-positive bacteria. These conjugates thus show a broad-spectrum activity, which is absent in CRAMP or vancomycin alone, and which is strongly improved compared to an equimolar mixture of CRAMP and vancomycin. In addition, these conjugates also show a strong inhibitory activity against S. Typhimurium biofilm formation.

Synthesis of 8-hydroxy-2-iminochromene derivatives as selective and potent inhibitors of human carbonyl reductase 1 by Dawei Hu; Namiki Miyagi; Yuki Arai; Hiroaki Oguri; Takeshi Miura; Toru Nishinaka; Tomoyuki Terada; Hiroaki Gouda; Ossama El-Kabbani; Shuang Xia; Naoki Toyooka; Akira Hara; Toshiyuki Matsunaga; Akira Ikari; Satoshi Endo (7487-7499).
Human carbonyl reductase 1 (CBR1), a member of the short-chain dehydrogenase/reductase superfamily, reduces anthracycline anticancer drugs to their less potent anticancer C-13 hydroxy metabolites, which are linked with pathogenesis of cardiotoxicity, a side effect of the drugs. CBR1 inhibitors are thought to be promising agents for adjuvant therapy with a twofold beneficial effect in prolonging the anticancer efficacy of the anthracyclines while decreasing cardiotoxicity. In order to search for new potential inhibitors of CBR1, we synthesized a series of des-methoxyphenyl derivatives of (Z)-2-(4-methoxyphenylimino)-7-hydroxy-N-(pyridin-2-yl)-2H-chromene-3-carboxamide (1) that was developed previously as a potent inhibitor of aldo-keto reductase (AKR) 1B10 and AKR1B1. Among the newly synthesized inhibitors, 8-hydroxy-2-imino-2H-chromene-3-carboxylic acid (2-chlorophenyl)amide (13h) was the most potent competitive inhibitor of CBR1, showing a Ki value of 15 nM. 13h also showed high selectivity to CBR1 over its isozyme CBR3 and other enzymes with CBR activity (AKR1B1, AKR1B10, AKR1C1, AKR1C2, AKR1C4, DXCR and DHRS4). Furthermore, 13h inhibited the cellular metabolism by CBR1 at its concentration of 4 μM. The structure–activity relationship of the derivatives, site-directed mutagenesis of putative binding residues (Met141 and Trp229) and molecular docking of 13h in CBR1 revealed that the interactions of 13h with the substrate-binding residues (Ser139, Met141, Tyr193 and Trp229) are important for the tight binding.

Interaction of myo-inositol hexakisphosphate with biogenic and synthetic polyamines by Julia Torres; Claudia Giorgi; Nicolás Veiga; Carlos Kremer; Antonio Bianchi (7500-7512).
Within all the eukaryotic cells myo-inositol phosphates (InsPs) are an important group of biomolecules that are potentially related to signaling functions. The most abundant member of this family in nature is InsP6 (phytate, L12− in its fully deprotonated form). The complicated chemical behavior of this molecule demands a great effort to understand its function in the cell medium. In this work we follow our earlier studies on the interaction of InsP6 with metal cations by inclusion of polyamines (both biogenic and synthetic) as potential agents to produce stable adducts. The stability constants of InsP6–amine adducts and the relevant thermodynamic parameters ΔG°, ΔH°, and ΔS° were determined at 37.0 °C and 0.15 M ionic strength by means of potentiometric titrations and isothermal titration calorimetry (ITC). The biogenic amines studied were 1,4-diaminobutane (putrescine, put), 1,5-diaminopentane (cadaverine, cad), N-(3-aminopropyl)-1,4-diaminobutane (spermidine, spd), N,N′-bis(3-aminopropyl)-1,4-diaminobutane (spermine, spm), and 1-(4-aminobutyl)guanidine (agmatine, agm), while the synthetic models of longer polyamines were 1,19-dimethyl-1,4,7,10,13,16,19-heptaazanonadecane (Me2hexaen), 1,22-dimethyl-1,4,7,10,13,16,19,22-octaazadocosane (Me2heptaen), 1,25-dimethyl-1,4,7,10,13,16,19,22,25-nonaazapentacosane (Me2octaen) and N,N′-bis(3-aminopropyl)-1,3-propanediamine (3,3,3-tet). With the aid of molecular modeling, we also studied the structural aspects of molecular recognition in operation. The final result is a balance between many parameters including charge of the species, flexibility of the amines, H-bonds in the adduct, and desolvation processes.

Highly enantioselective asymmetric transfer hydrogenation (ATH) of α-phthalimide ketones by Zhou Xu; Yong Li; Jing Liu; Nan Wu; Ke Li; Songlei Zhu; Rongli Zhang; Yi Liu (7513-7516).
A mild catalyst system for the synthesis of chiral amino alcohols via asymmetric transfer hydrogenation (ATH) of α-phthalimide ketones has been developed by using a chiral Ru-TsDPEN complex as the catalyst in DMF/MeOH at 40 °C. The reaction exhibits high reaction activity and excellent enantioselectivity where up to 96% yield and 99% ee of the product were obtained.

Synthesis and evaluation of a novel Rhodamine B pyrene [2]rotaxane as an intracellular delivery agent for doxorubicin by Jiaxin Shi; Yuan Xu; Xinlong Wang; Luyong Zhang; Jing Zhu; Tao Pang; Xiaofeng Bao (7517-7529).
A novel Rhodamine B-derivatized host [2]rotaxane, containing a dibenzyl-24-crown-8 (DB24C8) ring as the wheel and a pyrene as another fluorophore blocking group, was designed, synthesized and structurally characterized. A comparison of the 1H NMR spectra of RhBPy [2]rotaxane with those of 2 and DB24C8, nuclear Overhauser effect spectroscopy (NOESY), mass spectrometry and fluorescence spectroscopy confirmed the interlocked nature of RhBPy [2]rotaxane. The temperature dependence of the rotaxane studied by 1H NMR spectroscopy further demonstrated that RhBPy [2]rotaxane can be applied as a molecular switch. RhBPy [2]rotaxane has also been demonstrated to be an efficient transport agent for delivering the cancer drug doxorubicin (DOX) into tumor cells. Indeed, DOX delivered by RhBPy [2]rotaxane could effectively inhibit tumor cell growth.

Design, synthesis and biological evaluation of novel dimeric and tetrameric cRGD–paclitaxel conjugates for integrin-assisted drug delivery by A. Bianchi; D. Arosio; P. Perego; M. De Cesare; N. Carenini; N. Zaffaroni; M. De Matteo; L. Manzoni (7530-7541).
Integrins are associated with tumour cell survival and progression, and their expression has been shown to be increased in tumours. Thus, four novel conjugates of the tripeptide integrin ligand Arg-Gly-Asp (RGD) and the cytotoxic agent paclitaxel (cRGD–PTX) were prepared to investigate the potential of the multivalent presentation of the RGD moiety in improving the antitumor efficacy of PTX by tumour targeting. PTX was conjugated to two or four integrin recognizing ligands. The influence of multivalent presentation on in vitroαvβ3-receptor affinity was confirmed. For all the conjugates compared to the previously synthesized monovalent counterparts, an enhancement of the binding strength was observed; this behaviour was more pronounced when considering the tetravalent presented RGD-conjugate. Cell growth inhibition assays on a panel of human tumour cell lines showed remarkable cytotoxic activity for all conjugates with IC50 values in a nanomolar range. Among the four conjugates, the bivalent derivative 3b was selected for in vivo studies in an ovarian carcinoma cell model xenografted in immunodeficient mice. A marked antitumor activity was observed, similar to that of PTX, but with a much more favourable toxicity profile. Overall, the novel cRGD–PTX conjugates disclosed here represent promising candidates for further advancement in the domain of targeted anti-tumour therapy.

Synthesis of 2-deoxy-2,2-difluoro-α-maltosyl fluoride and its X-ray structure in complex with Streptomyces coelicolor GlgEI-V279S by Sandeep Thanna; Jared J. Lindenberger; Vishwanath V. Gaitonde; Donald R. Ronning; Steven J. Sucheck (7542-7550).
Streptomyces coelicolor (Sco) GlgEI is a glycoside hydrolase involved in α-glucan biosynthesis and can be used as a model enzyme for structure-based inhibitor design targeting Mycobacterium tuberculosis (Mtb) GlgE. The latter is a genetically validated drug target for the development of anti-Tuberculosis (TB) treatments. Inhibition of Mtb GlgE results in a lethal buildup of the GlgE substrate maltose-1-phosphate (M1P). However, Mtb GlgE is difficult to crystallize and affords lower resolution X-ray structures. Sco GlgEI-V279S on the other hand crystallizes readily, produces high resolution X-ray data, and has active site topology identical to Mtb GlgE. We report the X-ray structure of Sco GlgEI-V279S in complex with 2-deoxy-2,2-difluoro-α-maltosyl fluoride (α-MTF, 5) at 2.3 Å resolution. α-MTF was designed as a non-hydrolysable mimic of M1P to probe the active site of GlgE1 prior to covalent bond formation without disruption of catalytic residues. The α-MTF complex revealed hydrogen bonding between Glu423 and the C1F which provides evidence that Glu423 functions as proton donor during catalysis. Further, hydrogen bonding between Arg392 and the axial C2 difluoromethylene moiety of α-MTF was observed suggesting that the C2 position tolerates substitution with hydrogen bond acceptors. The key step in the synthesis of α-MDF was transformation of peracetylated 2-fluoro-maltal 1 into peracetylated 2,2-difluoro-α-maltosyl fluoride 2 in a single step via the use of Selectfluor®.

Tryptophan prenyltransferases FgaPT2, 5-DMATS, 6-DMATSSv and 7-DMATS catalyse regiospecific C-prenylations on the indole ring, while tyrosine prenyltransferases SirD and TyrPT catalyse the O-prenylation of the phenolic hydroxyl group. In this study, we report the Friedel–Crafts alkylation of l-o-tyrosine by these enzymes. Surprisingly, no conversion was detected with SirD and three tryptophan prenyltransferases showed significantly higher activity than another tyrosine prenyltransferase TyrPT. C5-prenylated l-o-tyrosine was identified as a unique product of these enzymes. Using l-m-tyrosine as the prenylation substrate, product formation was only observed with the tryptophan prenyltransferases FgaPT2 and 7-DMATS. C4- and C6-prenylated derivatives were identified in the reaction mixture of FgaPT2. These results provided additional evidence for the similarities and differences between these two subgroups within the DMATS superfamily in their catalytic behaviours.

In the present study, mechanistic insights into the domino reaction between 1,4-dithiane-2,5-diol and azomethine imines were derived from the computational study with B3LYP and M06-2X functionals. On the whole, the domino process comprises two consecutive reactions: cleavage of 1,4-dithiane-2,5-diol leading to mercaptoacetaldehyde and [3 + 3] cycloaddition of mercaptoacetaldehyde with azomethine imines. The cleavage of 1,4-dithiane-2,5-diol can take place via multiple possible pathways (1A–1E), and pathway 1E in which double-methanol molecules mediate the proton transfer process is the most energetically favorable, with an energy barrier of 19.9 kcal mol−1. For the [3 + 3] cycloaddition, three possible pathways (2F–2H) were explored. The calculated energy profiles reveal that pathway 2H with activation energies ranging from 6.9 to 10.2 kcal mol−1 is more energetically favorable than pathways 2F and 2G. Specifically, pathway 2H comprises three reaction steps: deprotonation of mercaptoacetaldehyde by DABCO allows for the formation of the thiol anion, which subsequently launches a nucleophilic attack on azomethine imines followed by intramolecular cyclization resulting in the final products. The calculated results are in agreement with the experimental observations that the reaction can proceed most efficiently in the presence of both DABCO and methanol. Furthermore, the hydrogen bonding interaction is identified to be the main factor determining the observed diastereoselectivity The current systematic theoretical study gives a full scenario of the reaction between 1,4-dithiane-2,5-diol and azomethine imines catalyzed by DABCO, and thus provides some valuable clues for further investigation and development of this kind of important reaction.

Back cover (7571-7572).