Organic & Biomolecular Chemistry (v.16, #34)

Front cover (6159-6160).

Contents list (6161-6167).

Target-protein-selective inactivation and labelling using an oxidative catalyst by Shinichi Sato; Michihiko Tsushima; Hiroyuki Nakamura (6168-6179).
Reactive oxygen species (ROS) and radical species generated using oxidative single-electron transfer (SET) catalysts are highly reactive, inducing local environmental oxidative reactions, resulting in protein inactivation and labelling in proximity to the catalysts. Oxidative catalysts bound to the target protein generate ROS which induce oxidation only within a limited radius (∼30 nm), resulting in target-protein-selective inactivation. On the other hand, protein chemical labelling reactions via ROS or SET induced by the catalysts are completed in proximity to the catalyst. These proximity labelling techniques have recently attracted considerable attention as innovative tools to elucidate protein interaction mapping and unknown protein–protein interaction (PPI) partners. Not only can peroxidases be genetically introduced into the protein of interest but also ligand-conjugated catalysts can catalyze oxidative SET reactions in a protein mixture under intracellular conditions. In this review, we focus on two approaches of selective inactivation of protein functions and selective protein labelling using oxidative SET catalysts.

Phosphite-catalyzed alkoxycarbonylation of aryl diazonium salts by Jian-Xing Xu; Robert Franke; Xiao-Feng Wu (6180-6182).
In this communication, an interesting phosphite-catalyzed alkoxycarbonylation of aryl diazonium salts has been reported. At room temperature and under CO pressure, moderate to good yields of the desired esters can be produced in the absence of bases or any other additives.

The design and synthesis of a new chiral monodentate spiro phosphoramidite ligand based on a hexamethyl-1,1′-spirobiindane scaffold has been accomplished. The ligand could serve as an elegant chiral monodentate ligand in the Pd-catalyzed asymmetric hydroamination/arylation of alkenes leading to chiral imidazolidin-2-ones with good enantioselectivities.

A stereoselective debromoborylation of aliphatic 1,1-dibromo-1-alkenes to prepare (Z)-1-bromo-1-alkenylboronate esters using copper(i) catalysts was developed. The debromoborylation of various aliphatic 1,1-dibromo-1-alkenes in the presence of a copper(i) catalyst and bis(pinacolato)diboron proceeded smoothly to produce (Z)-1-bromo-1-alkenylboronate esters in good yields with only Z geometry.

Silver-catalyzed intermolecular amination of fluoroarenes by Yu Wang; Chenlong Wei; Ruyun Tang; Haosheng Zhan; Jing Lin; Zhenhua Liu; Weihua Tao; Zhongxue Fang (6191-6194).
A novel highly selective Ag-catalyzed intermolecular amination of fluoroarenes has been developed. This transformation starts from readily available 4-carbonyl fluorobenzene and NaN3 or other nitrogen-source, via amination followed by C–F bond cleavage, thus affording the desired 4-carbonyl arylamine products under mild conditions. The reaction is accelerated using a small amount of water. This pathway is distinct from a previously reported radical amination reaction.

Molecular engineering of logic gate types by module rearrangement in ‘Pourbaix Sensors’: the effect of excited-state electric fields by Jake C. Spiteri; Sergey A. Denisov; Gediminas Jonusauskas; Sylwia Klejna; Konrad Szaciłowski; Nathan D. McClenaghan; David C. Magri (6195-6201).
Two types of fluorescent logic gates are accessed from two different arrangements of the same modular components, one as an AND logic gate (1) and the other as a PASS 0 logic gate (2). The logic gates were designed with an ‘electron-donor–spacer1–fluorophore–spacer2–receptor’ format and demonstrated in 1 : 1 (v/v) methanol/water. The molecules consist of ferrocene as the electron donor, 4-aminonaphthalimide as the fluorophore and a tertiary alkylamine as the receptor. In the presence of high H+ and Fe3+ levels, regioisomers 1a and 1b switch ‘on’ as AND logic gates with fluorescence enhancement ratios of 16-fold and 10-fold, respectively, while regioisomers 2a and 2b are functionally dormant, exhibiting no fluorescence switching. The PASS 0 logic of 2a and 2b results from the transfer of an electron from the excited state fluorophore to the ferrocenium unit under oxidising conditions as predicted by DFT calculations. Time-resolved fluorescence spectroscopy provided lifetimes of 8.3 ns and 8.1 ns for 1a and 1b, respectively. The transient signal recovery rate of 1b is ∼10 ps while that of 2b is considerably longer on the nanosecond timescale. The divergent logic attributes of 1 and 2 highlight the importance of field effects and opens up a new approach for regulating logic-based molecules.

TsOH·H2O-mediated N-amidation of quinoline N-oxides: facile and regioselective synthesis of N-(quinolin-2-yl)amides by Xinghua Chen; Mei Peng; Hao Huang; Yangfan Zheng; Xiaojun Tao; Chunlian He; Yi Xiao (6202-6205).
An operationally simple method with 100% atom economy has been developed for the synthesis of various N-(quinolin-2-yl)amides via the TsOH·H2O-mediated N-amidation of quinoline N-oxides using inexpensive and commercially available nitriles as the amidation reagents. Mechanistic exploration suggested that the reaction probably proceeds through an acid-assisted 1,3-dipolar cycloaddition and an N–O bond cleavage followed by a dehydro-aromatization process.

Molecular tweezers with a rotationally restricted linker and freely rotating porphyrin moieties by Rhys B. Murphy; Duc-Truc Pham; Jonathan M. White; Stephen F. Lincoln; Martin R. Johnston (6206-6223).
The effect of the degree of conformational rigidity and/or flexibility on preorganisation in artificial molecular receptors continues to be actively explored by supramolecular chemists. This work describes a bis-porphyrin architecture, linked via a rigid polycyclic backbone, in which a sterically bulky 2,3,5,6-tetramethylphenyl diimide core restricts rotation to afford two non-interconvertible tweezer conformations; syn- and anti-. After separation, the host–guest chemistry of each conformation was studied independently. The difference in host geometry allows only the syn-conformation to form a strong 1 : 1 bis-porphyrin complex with the diamino ligand 1,4-diazabicyclo[2.2.2]octane (DABCO) (K11 = 1.25 × 108 M−1), with the anti-conformation adopting a 2 : 2 sandwich complex with DABCO (K22 = 5.57 × 1017 M−3).

A modular synthesis of aspulvinones A, B, C, D, E, G and the recently isolated aspulvinone Q was developed. The methodology features a highly stereoselective aldol condensation of diazotetronic acid with aldehydes to provide 5-arylidene diazotetronates. Subsequent catalytic intermolecular C–H insertion reactions of the arylidene tetronates with arenes provide a series of naturally occurring aspulvinones including aspulvinones C, D and Q which have not been synthesized before. Variation of the aldehyde and the arene components furnishes synthetic analogues of the aspulvinones.

The folate pathway is a recognized intervention point for treating parasitic and bacterial infections in humans. However, the efficacy of treatments targeting dihydropteroate synthase (DHPS) and dihydrofolate reductase (DHFR) has reduced due to disease-related mutations. This has prompted interest in other enzyme targets on this clinically validated pathway, including 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK). A challenge in the design of molecules to target this enzyme is that the precise mechanism of the reaction and the role of the active site residues are not fully understood. In this study, we report the first theoretical analysis of the catalytic pathway of the natural substrate using hybrid quantum mechanical/molecular mechanical (QM/MM) methods. The reaction profiles associated with three proposed general bases have been investigated, as well as the profile for two mutant enzymes, namely R92A and R82A. We identified R92 as the general base in the wildtype reaction. The predicted barriers are in good agreement with the observed experimental kcat values obtained for wildtype and mutant proteins.

Divergent synthesis of new α-glucosidase inhibitors obtained through a vinyl Grignard-mediated carbocyclisation by Ida M. B. Knudsen; Christinne Hedberg; Lucy Kate Ladefoged; Daisuke Ide; Anne Brinkø; Espen Z. Eikeland; Atsushi Kato; Henrik H. Jensen (6250-6261).
Four new α-glucosidase inhibitors have been synthesised through 5–8 synthetic steps from a common synthetic intermediate obtained through a recently developed carbocyclisation. The compounds were designed as hybrids of the known glucosidase inhibitors valienamine, voglibose and miglitol. All four compounds showed activity against rat intestinal sucrase with the most potent inhibitor acting at low micromolar concentration. The newly synthesised compounds were not as potent as miglitol against sucrase but showed greater selectivity towards the tested glycosidases. The most potent inhibitors were docked into a homology model built for this study of rat intestinal sucrase explaining the difference in potency between two diastereoisomers with varying orientation of a secondary amine.

Building of neomycin–nucleobase–amino acid conjugates for the inhibition of oncogenic miRNAs biogenesis by Duc Duy Vo; Cécile Becquart; Thi Phuong Anh Tran; Audrey Di Giorgio; Fabien Darfeuille; Cathy Staedel; Maria Duca (6262-6274).
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers, thus being oncogenic. The inhibition of oncogenic miRNAs (defined as the blocking of miRNAs’ production or function) would find application in the therapy of different types of cancer in which these miRNAs are implicated. In this work, we describe the design and synthesis of new small-molecule RNA ligands with the aim of inhibiting Dicer-mediated processing of oncogenic miRNAs. One of the synthesized compound (4b) composed of the aminoglycoside neomycin conjugated to an artificial nucleobase and to amino acid histidine is able to selectively decrease miR-372 levels in gastric adenocarcinoma (AGS) cells and to restore the expression of the target LATS2 protein. This activity led to the inhibition of proliferation of these cells. The study of the interactions of 4b with pre-miR-372 allowed for the elucidation of the molecular mechanism of the conjugate, thus leading to new perspectives for the design of future inhibitors.

Iodine-mediated cross-dehydrogenative coupling of pyrazolones and alkenes by Kai Yang; Xiaoze Bao; Ye Yao; Jingping Qu; Baomin Wang (6275-6283).
An iodine-mediated alkenylation of pyrazolones with simple alkenes under an air atmosphere has been developed. By this protocol, the pharmaceutically relevant pyrazolone scaffold was directly adorned with a readily transformable olefinic functional group through a cross-dehydrogenative coupling process in moderate to excellent yields. The coupling products could be facilely manipulated by, for example, the Heck reaction and hydrogenation treatment, thus enriching the pyrazolone derivatives. Based on the observation of the reaction intermediate and mechanistical experiments, two possible reaction pathways were proposed.

Palladium-catalyzed direct mono-aroylation of O-arylmethyl and aryl-substituted acetoxime ethers by Ling-Yan Shao; Zhi Xu; Cun-Ying Wang; Xiao-Pan Fu; Miao-Miao Chen; Hong-Wei Liu; Ya-Fei Ji (6284-6294).
An efficient palladium-catalyzed ortho-aroylation of O-arylmethyl and aryl-substituted acetoxime ethers has been developed; this method has high mono-site selectivity and does not require exogenous ligands. Under the direction of a simple exo-acetoxime auxiliary, a broad scope of masked arylmethyl alcohols and phenols as well as various aromatic aldehydes are compatible with this transformation, which probably follows a mechanistic pathway involving a six- or five-membered exo-cyclopalladated intermediate. The strategy can be expediently adopted to prepare synthetically valuable 1H-benzo[d][1,2]oxazines and benzo[d]isoxazoles. The directing group can be easily removed from the products to afford the functionalized diaryl ketones.

Quinoline–galactose hybrids bind selectively with high affinity to a galectin-8 N-terminal domain by Kumar Bhaskar Pal; Mukul Mahanti; Xiaoli Huang; Stella Persson; Anders P. Sundin; Fredrik R. Zetterberg; Stina Oredsson; Hakon Leffler; Ulf J. Nilsson (6295-6305).
Quinolines, indolizines, and coumarins are well known structural elements in many biologically active molecules. In this report, we have developed straightforward methods to incorporate quinoline, indolizine, and coumarin structures into galactoside derivatives under robust reaction conditions for the discovery of glycomimetic inhibitors of the galectin family of proteins that are involved in immunological and tumor-promoting biological processes. Evaluation of the quinoline, indolizine and coumarin-derivatised galactosides as inhibitors of the human galectin-1, 2, 3, 4N (N-terminal domain), 4C (C-terminal domain), 7, 8N, 8C, 9N, and 9C revealed quinoline derivatives that selectively bound galectin-8N, a galectin with key roles in lymphangiogenesis, tumor progression, and autophagy, with up to nearly 60-fold affinity improvements relative to methyl β-d-galactopyranoside. Molecular dynamics simulations proposed an interaction mode in which Arg59 had moved 2.5 Å and in which an inhibitor carboxylate and quinoline nitrogen formed structure-stabilizing water-mediated hydrogen bonds. The compounds were demonstrated to be non-toxic in an MTT assay with several breast cancer cell lines and one normal cell line. The improved affinity, selectivity, and low cytotoxicity suggest that the quinoline–galactoside derivatives provide an attractive starting point for the development of galectin-8N inhibitors potentially interfering with pathological lymphangiogenesis, autophagy, and tumor progression.

Native chemical ligation at methionine bioisostere norleucine allows for N-terminal chemical protein ligation by Bo-Tao Xin; Bianca D. M. van Tol; Huib Ovaa; Paul P. Geurink (6306-6315).
The development of γ-thionorleucine (ThioNle) as a handle for native chemical ligation–desulfurization is reported here. ThioNle is a new addition to the expanding thiolated amino acid toolbox and serves as a methionine substitute in NCL with the advantage that it lacks the undesirable oxidation-prone thioether moiety. Its usefulness for N-terminal ubiquitination is demonstrated by efficient preparation of fully synthetic linear diubiquitin with preserved protein folding compared to the expressed material. Interestingly, gel-based deubiquitinating assays revealed that the methionine to norleucine substitution did affect diubiquitin cleavage, which may indicate a more profound role for methionine in the interaction between ubiquitin and the deubiquitinating enzymes than has been known so far.

Cesium carbonate-promoted synthesis of aryl methyl sulfides using S-methylisothiourea sulfate under transition-metal-free conditions by Caiyang Zhang; You Zhou; Jintao Huang; Canhui Tu; Xiaoai Zhou; Guodong Yin (6316-6321).
In the presence of cesium carbonate, an efficient synthesis of aryl methyl sulfides by the reactions of aryl halides with commercially available S-methylisothiourea sulfate is developed. This odourless and highly crystalline solid can be used as the substitute for malodorous methanethiol. The gram-scale reaction also proceeds smoothly without the use of column chromatography separation. Similarly, 2-(dimethylamino)ethylthio and cyclopropylmethylthio groups can be easily introduced into the aromatic rings from the corresponding S-[2-(dimethylamino)ethyl]isothiourea dihydrochloride and S-cyclopropylmethylisothiourea hydrobromide. The possible reaction mechanism is proposed. It is believed that this route to aryl alkyl sulfides is well competitive with currently known methods due to its wide substrate scope, excellent yields, easy operation and transition-metal-free conditions.

A robust ligand-free palladium-catalyzed cascade reaction for the synthesis of diversely substituted iminoisoindolinones has been developed. The cascade reaction involves isocyanide insertion into Ugi-3CR adducts, accompanied by unexpected hydroxylation and rearrangement.

Rational design of a highly reactive dicysteine peptide tag for fluorogenic protein labelling by Miroslava Strmiskova; Kelvin Tsao; Jeffrey W. Keillor (6332-6340).
Rationally designed libraries of a short helical peptide sequence containing two cysteine residues were screened kinetically for their reactivity towards complementary dimaleimide fluorogens. This screening revealed variant sequences whose reactivity has been increased by an order of magnitude relative to the original sequence. The most reactive engineered sequences feature mutant residues bearing positive charges, suggesting the pKa values of the adjacent thiol groups have been significantly lowered, through electrostatic stabilization of the thiolate ionization state. pH-Rate profiles measured for several mutant sequences support this mechanism of rate enhancement. The practical utility of the enhanced reactivity of the final engineered dicysteine tag (‘dC10*’) was then demonstrated in the fluorogenic intracellular labelling of histone H2B in living HeLa cells.

trans-Hydroboration vs. 1,2-reduction: divergent reactivity of ynones and ynoates in Lewis-base-catalyzed reactions with pinacolborane by You Zi; Fritz Schömberg; Fabian Seifert; Helmar Görls; Ivan Vilotijevic (6341-6349).
Ynones and ynoates react with pinacolborane in a divergent manner in the presence of nucleophilic phosphine catalysts. Ynones are transformed to the corresponding propargyl alcohols in good yields with high regio- and chemoselectivity. Ynoates undergo highly regio- and stereoselective trans-hydroboration to produce E-vinylboronates. Impressive divergence in reactivity of ynones and ynoates can be traced back to the mechanistic aspects of 1,2-reduction and trans-hydroboration. A comparative analysis of the two pathways paints a complex picture in which different reaction rates control selectivity in these seemingly unrelated processes and explains how sufficiently acidic protons in the reaction mixtures can be used to steer the selectivity in different directions.

An off–on fluorescent probe for the detection of mitochondria-specific protein persulfidation by Wenqi Meng; Yongchun Chen; Yongwei Feng; Hao Zhang; Qingqiang Xu; Mingxue Sun; Wenwen Shi; Jinfeng Cen; Jie Zhao; Kai Xiao (6350-6357).
Protein persulfidation is a newly defined oxidative posttranslational modification and plays important roles in many biological processes. Detection of protein persulfidation in living systems is urgently needed to advance the study of H2S/H2Sn-based signalling and cellular redox regulation. Here, we developed a novel off–on fluorescent probe for the detection of persulfidation using a chemical sensor, HQO-SSH, in biological systems. HQO-SSH features fast reaction, good selectivity and high sensitivity. Due to the distinctive features of HQO-SSH, this probe was successfully applied to image protein persulfidation changes in pulmonary cells. We also demonstrated that the probe is suitable for imaging protein persulfidation in lung tissues. In addition, confocal imaging with this method revealed that sulfur mustard, a commonly used chemical warfare agent, decreased mitochondrial protein persulfidation in living lung cells and tissues. Due to these results, this probe holds great promise for exploring the role of protein persulfidation in a variety of pathophysiological conditions.

Back cover (6359-6360).