Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities.

Histone deacetylases (HDACs) are validated targets for treatment of certain cancer types and play numerous regulatory roles in biology, ranging from epigenetics to metabolism. Small molecules are highly important as tool compounds for probing these mechanisms as well as for the development of new medicines. Therefore, detailed mechanistic information and precise characterization of the chemical probes used to investigate the effects of HDAC enzymes are vital. We interrogated Nature's arsenal of macrocyclic nonribosomal peptide HDAC inhibitors by chemical synthesis and evaluation of more than 30 natural products and analogues. This furnished surprising trends in binding affinities for the various macrocycles, which were then exploited for the design of highly potent class I and IIb HDAC inhibitors. Furthermore, thorough kinetic investigation revealed unexpected inhibitory mechanisms of important tool compounds as well as the approved drug Istodax (romidepsin). This work provides novel inhibitors with varying potencies, selectivity profiles, and mechanisms of inhibition and, importantly, affords insight into known tool compounds that will improve the interpretation of their effects in biology and medicine.

Synthetic Applications and Mechanistic Studies of the Hydroxide-Mediated Cleavage of Carbon-Carbon Bonds in Ketones.

The hydroxide-mediated cleavage of ketones into alkanes and carboxylic acids has been reinvestigated and the substrate scope extended to benzyl carbonyl compounds. The transformation is performed with a 0.05 M ketone solution in refluxing xylene in the presence of 10 equiv of potassium hydroxide. The reaction constitutes a straightforward protocol for the synthesis of certain phenyl-substituted carboxylic acids from 2-phenylcycloalkanones. The mechanism was investigated by kinetic experiments which indicated a first order reaction in hydroxide and a full negative charge in the rate-determining step. The studies were complemented by a theoretical investigation where two possible pathways were characterized by DFT/M06-2X. The calculations showed that the scission takes place by nucleophilic attack of hydroxide on the ketone followed by fragmentation of the resulting oxyanion into the carboxylic acid and a benzyl anion.

New Motifs in Deoxydehydration: Beyond the Realms of Rhenium.

The deoxydehydration (DODH) reaction remains one of the most efficient methods of reducing the oxygen content of biomass while keeping important functionality in place. This reaction is traditionally catalysed by high-valent oxo-rhenium species. Recent research into heterogeneous rhenium-based catalysts for DODH demonstrates their ability to rival and in some cases surpass their homogeneous counterparts. Furthermore, catalysts based on the metals molybdenum and vanadium show great potential as inexpensive alternatives to rhenium catalysts. In this Minireview, we detail the recent developments within the field of DODH with particular emphasis on discoveries outside the realms of rhenium.

Enolonium Species-Umpoled Enolates.

Enolonium species/iodo(III)enolates of carbonyl compounds have been suggested to be intermediates in a wide variety of hypervalent iodine induced chemical transformations of ketones, including α-C-O, α-C-N, α-C-C, and α-carbon-halide bond formation, but they have never been characterized. We report that these elusive umpoled enolates may be made as discrete species that are stable for several minutes at -78 °C, and report the first spectroscopic identification of such species. It is shown that enolonium species are direct intermediates in C-O, C-N, C-Cl, and C-C bond forming reactions. Our results open up chemical space for designing a variety of new transformations. We showcase the ability of enolonium species to react with prenyl, crotyl, cinnamyl, and allyl silanes with absolute regioselectivity in up to 92 % yield.

Mechanistic Investigation of Molybdate-Catalysed Transfer Hydrodeoxygenation.

The molybdate-catalysed transfer hydrodeoxygenation (HDO) of benzyl alcohol to toluene driven by oxidation of the solvent isopropyl alcohol to acetone has been investigated by using a combination of experimental and computational methods. A Hammett study that compared the relative rates for the transfer HDO of five para-substituted benzylic alcohols was carried out. Density-functional theory (DFT) calculations suggest a transition state with significant loss of aromaticity contributes to the lack of linearity observed in the Hammett study. The transfer HDO could also be carried out in neat PhCH2 OH at 175 °C. Under these conditions, PhCH2 OH underwent disproportionation to yield benzaldehyde, toluene, and significant amounts of bibenzyl. Isotopic-labelling experiments (using PhCH2 OD and PhCD2 OH) showed that incorporation of deuterium into the resultant toluene originated from the α position of benzyl alcohol, which is in line with the mechanism suggested by the DFT study.

Dehydrogenative Synthesis of Carboxylic Acids from Primary Alcohols and Hydroxide Catalyzed by a Ruthenium N-Heterocyclic Carbene Complex.

Primary alcohols have been reacted with hydroxide and the ruthenium complex [RuCl2(IiPr)(p-cymene)] to afford carboxylic acids and dihydrogen. The dehydrogenative reaction is performed in toluene, which allows for a simple isolation of the products by precipitation and extraction. The transformation can be applied to a range of benzylic and saturated aliphatic alcohols containing halide and (thio)ether substituents, while olefins and ester groups are not compatible with the reaction conditions. Benzylic alcohols undergo faster conversion than other substrates, and a competing Cannizzaro reaction is most likely involved in this case. The kinetic isotope effect was determined to be 0.67 using 1-butanol as the substrate. A plausible catalytic cycle was characterized by DFT/B3LYP-D3 and involved coordination of the alcohol to the metal, ß-hydride elimination, hydroxide attack on the coordinated aldehyde, and a second ß-hydride elimination to furnish the carboxylate.

Shape-selective Valorization of Biomass-derived Glycolaldehyde using Tin-containing Zeolites.

A highly selective self-condensation of glycolaldehyde to different C4 molecules has been achieved using Lewis acidic stannosilicate catalysts in water at moderate temperatures (40-100 °C). The medium-sized zeolite pores (10-membered ring framework) in Sn-MFI facilitate the formation of tetrose sugars while hindering consecutive aldol reactions leading to hexose sugars. High yields of tetrose sugars (74 %) with minor amounts of vinyl glycolic acid (VGA), an α-hydroxyacid, are obtained using Sn-MFI with selectivities towards C4 products reaching 97 %. Tin catalysts having large pores or no pore structure (Sn-Beta, Sn-MCM-41, Sn-SBA-15, tin chloride) led to lower selectivities for C4 sugars due to formation of hexose sugars. In the case of Sn-Beta, VGA is the main product (30 %), illustrating differences in selectivity of the Sn sites in the different frameworks. Under optimized conditions, GA can undergo further conversion, leading to yields of up to 44 % of VGA using Sn-MFI in water. The use of Sn-MFI offers multiple possibilities for valorization of biomass-derived GA in water under mild conditions selectively producing C4 molecules.

Theoretical Assessment of Fluorinated Phospholipids in the Design of Liposomal Drug-Delivery Systems.

Fluorinated phospholipid analogues are investigated as potential substrates for phospholipase A2 (PLA2) using classical molecular dynamics simulations and quantum mechanics/density functional theory calculations. The fluorinated phospholipid analogues are α-fluoro (HF-ProAEL) and α,α-difluoro (F2-ProAEL) conjugates of (R)-1-O-hexadecyl-2-palmitoyl-sn-glycero-3-phoshocholineglycerol (ProAEL). Our results provide a theoretical assessment of the potential usefulness of these fluorinated lipids in the rational design of liposomal drug-delivery systems. The α-fluorine-substituted phospholipid analogues are found to be substrates for secretory PLA2, with sufficient accessibility of water to the active site to allow for enzymatic hydrolysis. Because of the inherently less stable nature of HF-ProAEL and F2-ProAEL when compared to that of ProAEL, the hydrolytic reaction is predicted to occur at a progressively faster rate; the more electronegative substituent at the α-position effectively lowers the energy barrier for hydrolysis. We conclude that the partially fluorinated phospholipid analogues facilitate rational design of liposomal vesicles of phospholipid mixtures with desirable physicochemical properties and that are still subjects for important and pharmaceutically proven drug-delivery mechanisms.

Investigating the Sensitivity of NAD+-dependent Sirtuin Deacylation Activities to NADH.

Protein lysine posttranslational modification by an increasing number of different acyl groups is becoming appreciated as a regulatory mechanism in cellular biology. Sirtuins are class III histone deacylases that use NAD(+)as a co-substrate during amide bond hydrolysis. Several studies have described the sirtuins as sensors of the NAD(+)/NADH ratio, but it has not been formally tested for all the mammalian sirtuinsin vitro To address this problem, we first synthesized a wide variety of peptide-based probes, which were used to identify the range of hydrolytic activities of human sirtuins. These probes included aliphatic ϵ-N-acyllysine modifications with hydrocarbon lengths ranging from formyl (C1) to palmitoyl (C16) as well as negatively charged dicarboxyl-derived modifications. In addition to the well established activities of the sirtuins, "long chain" acyllysine modifications were also shown to be prone to hydrolytic cleavage by SIRT1-3 and SIRT6, supporting recent findings. We then tested the ability of NADH, ADP-ribose, and nicotinamide to inhibit these NAD(+)-dependent deacylase activities of the sirtuins. In the commonly used 7-amino-4-methylcoumarin-coupled fluorescence-based assay, the fluorophore has significant spectral overlap with NADH and therefore cannot be used to measure inhibition by NADH. Therefore, we turned to an HPLC-MS-based assay to directly monitor the conversion of acylated peptides to their deacylated forms. All tested sirtuin deacylase activities showed sensitivity to NADH in this assay. However, the inhibitory concentrations of NADH in these assays are far greater than the predicted concentrations of NADH in cells; therefore, our data indicate that NADH is unlikely to inhibit sirtuinsin vivo These data suggest a re-evaluation of the sirtuins as direct sensors of the NAD(+)/NADH ratio.

Spectroscopic Characterization of a Monomeric, Cyclopentadienyl-Based Rhenium(V) Dioxo Complex.

Mononuclear, coordinatively unsaturated rhenium(V) dioxo species of the type XReO2 (X = Me, substituted cyclopentadienyl) have long been postulated as intermediates in rhenium-catalyzed deoxydehydration, but their characterization was precluded because of aggregation into dimeric or oligomeric structures. Using the bulky 1,2,4-tri-tert-butylcyclopentadienyl (Cp(ttt)) ligand, the rhenium(V) dioxo species (Cp(ttt))ReO2 could now be observed, in equilibrium with the dimeric form [(Cp(ttt))Re(O)µ-O]2, and characterized by NMR, IR, and UV-vis spectroscopies, as well as electrospray ionization mass spectrometry. (Cp(ttt))ReO2 is shown to be the primary product of reduction of the rhenium(VII) complex (Cp(ttt))ReO3 with PPh3 and demonstrated to react with ethylene glycol significantly faster than its dimeric counterpart, supporting its role as an intermediate in rhenium-catalyzed deoxydehydration reactions.

Resolution and Determination of the Absolute Configuration of a Twisted Bis-Lactam Analogue of Tröger's Base: A Comparative Spectroscopic and Computational Study.

The first reported twisted bis-lactam, a racemic Tröger's base (TB) analogue (2), was resolved into its enantiomers on a chiral stationary phase HPLC column. The absolute configuration of (+)-2 was determined to be (R,R)-2 by comparing experimental and calculated vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectra. The absolute configuration of (-)-2 was determined by comparing experimental and calculated electronic circular dichroism (ECD) spectra. The corresponding theoretical spectra were calculated using the lowest energy conformation of (R,R)-2 and (S,S)-2 at the B3LYP/6-31G(d,p) level of theory. The absolute configuration of (+)-2 was also determined to (R,R)-2 by anomalous X-ray diffraction (AXRD) in a chiral space group P212121 using Cu-irradiation resulting in a very low Flack parameter of -0.06(3), despite the heaviest element being an oxygen atom, thus unambiguously confirming the results from the spectroscopic studies. We conclude that, for the Tröger's base (TB) analogue (2), we may rank the reliability of the individual methods for AC determination as AXRD ≫ VCD > ECD, while the synergy of all three methods provides very strong confidence in the assigned ACs of (+)-(R,R)-2 and (-)-(S,S)-2.

Triangular prism-shaped ß-peptoid helices as unique biomimetic scaffolds.

ß-Peptoids are peptidomimetics based on N-alkylated ß-aminopropionic acid residues (or N-alkyl-ß-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first time, that ß-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric ß-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6-9.8 Å between turns. The presence of folded conformations in solution is supported by circular dichroism spectroscopy showing length- and solvent dependency, and molecular dynamics simulations provide further support for a stabilized helical secondary structure in organic solvent. We thus outline a framework for future design of novel biomimetics that display functional groups with high accuracy in three dimensions, which has potential for development of new functional materials.

Oxidative umpolung α-alkylation of ketones.

We disclose a hypervalent iodine mediated α-alkylative umpolung reaction of carbonyl compounds with dialkylzinc as the alkyl source. The reaction is applicable to all common classes of ketones including 1,3-dicarbonyl compounds and regular ketones via their lithium enolates. The α-alkylated carbonyl products are formed in up to 93% yield. An ionic mechanism is inferred based on meticulous analysis, NMR studies, trapping and crossover experiments, and computational studies.

Tin-containing silicates: alkali salts improve methyl lactate yield from sugars.

This study focuses on increasing the selectivity to methyl lactate from sugars using stannosilicates as heterogeneous catalyst. All group I ions are found to have a promoting effect on the resulting methyl lactate yield. Besides, the alkali ions can be added both during the preparation of the catalyst or directly to the solvent mixture to achieve the highest reported yield of methyl lactate (ca. 75 %) from sucrose at 170 °C in methanol. The beneficial effect of adding alkali to the reaction media applies not only to highly defect-free Sn-Beta prepared through the fluoride route, but also to materials prepared by post-treatment of dealuminated commercial Beta zeolites, as well as ordered mesoporous stannosilicates, in this case Sn-MCM-41 and Sn-SBA-15. These findings open the door to the possibility of using other preparation methods or different Sn-containing silicates with equally high methyl lactate yields as Sn-Beta.

DFT study of the molybdenum-catalyzed deoxydehydration of vicinal diols.

The mechanism of the molybdenum-catalyzed deoxydehydration (DODH) of vicinal diols has been investigated using density functional theory. The proposed catalytic cycle involves condensation of the diol with an Mo(VI) oxo complex, oxidative cleavage of the diol resulting in an Mo(IV) complex, and extrusion of the alkene. We have compared the proposed pathway with several alternatives, and the results have been corroborated by comparison with the molybdenum-catalyzed sulfoxide reduction recently published by Sanz et al. and with experimental observations for the DODH itself. Improved understanding of the mechanism should expedite future optimization of molybdenum-catalyzed biomass transformations.

Rhenium-catalyzed deoxydehydration of diols and polyols.

The substitution of platform chemicals of fossil origin by biomass-derived analogues requires the development of chemical transformations capable of reducing the very high oxygen content of biomass. One such reaction, which has received increasing attention within the past five years, is the rhenium-catalyzed deoxydehydration (DODH) of a vicinal diol into an alkene; this is a model system for abundant polyols like glycerol and sugar alcohols. The present contribution includes a review of early investigations of stoichiometric reactions involving rhenium, diols, and alkenes followed by a discussion of the various catalytic systems that have been developed with emphasis on the nature of the reductant, the substrate scope, and mechanistic investigations.

Methyl effect in azumamides provides insight into histone deacetylase inhibition by macrocycles.

Natural, nonribosomal cyclotetrapeptides have traditionally been a rich source of inspiration for design of potent histone deacetylase (HDAC) inhibitors. We recently disclosed the total synthesis and full HDAC profiling of the naturally occurring azumamides ( J. Med. Chem. 2013 , 56 , 6512 ). In this work, we investigate the structural requirements for potent HDAC inhibition by macrocyclic peptides using the azumamides along with a series of unnatural analogues obtained through chemical synthesis. By solving solution NMR structures of selected macrocycles and combining these findings with molecular modeling, we pinpoint crucial enzyme-ligand interactions required for potent inhibition of HDAC3. Docking of additional natural products confirmed these features to be generally important. Combined with the structural conservation across HDACs 1-3, this suggests that while cyclotetrapeptides have provided potent and class-selective HDAC inhibitors, it will be challenging to distinguish between the three major class I deacetylases using these chemotypes.

A short designed semi-aromatic organic nanotube--synthesis, chiroptical characterization, and host properties.

The first generation of an organic nanotube based on the enantiomerically pure bicyclo[3.3.1]nonane framework is presented. The helical tube synthesised is the longest to date having its aromatic systems oriented parallel to the axis of propagation (length ∼26 Å and inner diameter ∼11 Å according to molecular dynamics simulations in chloroform). The synthesis of the tube, a heptamer, is based on a series of Friedländer condensations and the use of pyrido[3,2-d]pyrimidine units as masked 2-amino aldehydes, as a general means to propagate organic tubular structures and the introduction of a methoxy group for modification toward solubility and functionalization are described. The electronic CD spectra of the tube and molecular intermediates are correlated with theoretical spectra calculated with time-dependent density functional theory to characterize the chirality of the tube. Both experimental (NMR-titrations) and theoretical (molecular dynamics simulations) techniques are used to investigate the use of the tube as a receptor for the acetylcholine and guanidinium cations, respectively.

Molybdenum-catalyzed deoxydehydration of vicinal diols.

The commercially available (NH4 )6 Mo7 O24 and other molybdenum compounds are shown to be viable substitutes for the typically employed rhenium compounds in the catalytic deoxydehydration of aliphatic diols into the corresponding alkenes. The transformation, which represents a model system for the various hydroxyl groups found in biomass-derived carbohydrates, can be conducted in an inert solvent (dodecane), under solvent-free conditions, and in a solvent capable of dissolving biomass-derived polyols (1,5-pentanediol). The reaction is driven by the simultaneous oxidative deformylation of the diol resulting in an overall disproportionation of the substrate.

Synthesis of an orthogonal topological analogue of helicene.

The synthesis of an orthogonal topological pentamer analogue of helicene is presented. This analogue forms a tubular structure with its aromatic systems directed parallel to the axis of propagation, which creates a cavity with the potential to function as a host molecule. The synthetic strategy reported, based on a series of repeating Friedländer condensations that utilize pyrido[3,2-d]pyrimidine moieties as protected amino aldehydes, allows for the facile access of higher generations of helical, tubular structures. As a result of the synthetic strategy, only a helical isomer of the pentamer is possible. The structure and absolute configuration of the pentamer were elucidated from a combination of NMR spectroscopic data, optical properties, X-ray structures, and by comparison of an experimental electronic circular dichroism spectrum to a calculated spectrum.