Illustration of a computational pipeline for evaluating cyclodextrin host-guest complex formation through conformational capture of bullvalene.

Cyclodextrins have a diverse range of applications, including as supramolecular hosts, as enzyme active-site analogs, in improving drug solubility and delivery, and in molecular selection. We have investigated their ability to form stable complexes with bullvalenes, unusual organic cage molecules that spontaneously interconvert between numerous degenerate isomers. The shape-shifting nature of substituted bullvalenes raises the potential for dynamic adaptive binding to biological targets. We tested whether ß- and γ-cyclodextrins can capture particular bullvalene isomers and whether the preferred binding mode(s) differ between isomers. We first applied our computational host-guest interaction potential energy profiling to determine the best binding mode(s) of unsubstituted bullvalene and each isomer of methylenehydroxybullvalene to ß- and γ-cyclodextrin. Subsequent molecular dynamics simulations of the predicted host-guest complexes showed that while unsubstituted bullvalene has a single, albeit ill-defined, binding mode with either cyclodextrin, each isomer of methylenehydroxybullvalene has two possible modes of binding to ß-cyclodextrin but only a single, nebulous mode of binding to γ-cyclodextrin. Experimental determination of the binding free energy of each methylenehydroxybullvalene-cyclodextrin complex showed that methylenehydroxybullvalene is more likely to bind to ß-cyclodextrin than to γ-cyclodextrin, despite its smaller cavity. Together, our results suggest that ß-cyclodextrin, but not γ-cyclodextrin, shows promise for conformational capture of mono-substituted bullvalenes. More broadly, our computational pipeline should prove useful for rapid characterization of cyclodextrin host-guest complexes, avoiding the need for costly synthesis of guest molecules that are unlikely to bind stably, as well as providing detailed atomic-level insight into the nature of complexation.

Rapid functionalization of multiple C-H bonds in unprotected alicyclic amines.

The synthesis of valuable bioactive alicyclic amines containing variable substituents in multiple ring positions typically relies on multistep synthetic sequences that frequently require the introduction and subsequent removal of undesirable protecting groups. Although a vast number of studies have aimed to simplify access to such materials through the C-H bond functionalization of feedstock alicyclic amines, the simultaneous introduction of more than one substituent to unprotected amines has never been accomplished. Here we report an advance in C-H bond functionalization methodology that enables the introduction of up to three substituents in a single operation. Lithiated amines are first exposed to a ketone oxidant, generating transient imines that are subsequently converted to endocyclic 1-azaallyl anions, which can be processed further to furnish ß-substituted, α,ß-disubstituted, or α,ß,α'-trisubstituted amines. This study highlights the unique utility of in situ-generated endocyclic 1-azaallyl anions, elusive intermediates in synthetic chemistry.

Leishmanicidal Activity and Structure-Activity Relationships of Essential Oil Constituents.

Several constituents of essential oils have been shown to be active against pathogens such as bacteria, fungi, and protozoa. This study demonstrated the in vitro action of ten compounds present in essential oils against Leishmania amazonensis promastigotes. With the exception of p-cymene, all evaluated compounds presented leishmanicidal activity, exhibiting IC50 between 25.4 and 568.1 µg mL-1. Compounds with the best leishmanicidal activity presented a phenolic moiety (IC50 between 25.4 and 82.9 µg mL-1). Alicyclic alcohols ((-)-menthol and isoborneol) and ketones ((-)-carvone) promoted similar activity against the parasite (IC50 between 190.2 and 198.9 µg mL-1). Most of the compounds showed low cytotoxicity in L929 fibroblasts. Analysis of the structure-activity relationship of these compounds showed the importance of the phenolic structure for the biological action against the promastigote forms of the parasite.

Current Progresses and Trends in the Development of Progesterone Receptor Modulators.

The progesterone receptor (PR) is a ligand-activated steroid receptor in the nuclear receptor (NR) superfamily of transcription factor. Besides gynecological and obstetrical indications, the involvement/mechanism of PR in many other diseases, such as oncology, neurology, immunology, etc. has been revealed and studied in recent decades. Therapeutic agents that selectively activate or inhibit PR have been developed. PR agonists have generally been used in oral contraception and postmenopausal hormone replacement therapy (HRT), typically in combination with estrogens. PR antagonists and selective PR modulators (SPRMs) can be useful therapies for hormone dependent breast and prostate cancers, nonmalignant chronic conditions such as fibroids, and endometriosis. This review provides an overview and detailed discussions about the recent development of chemical structures of the PR ligands, their structural characteristics (particularly those contributing to their activity and selectivity), in vitro/in vivo studies and clinical trial outcomes, and the synthetic methodologies.

Synthesis and Biological Evaluation of Pentacycloundecylamines and Triquinylamines as Voltage-Gated Calcium Channel Blockers.

Preclinical studies for neurodegenerative diseases have shown a multi-targeted approach to be successful in the treatment of these complex disorders with several pathoetiological pathways. Polycyclic compounds, such as NGP1-01 (7a), have demonstrated the ability to target multiple mechanisms of the complex etiology and are referred to as multifunctional compounds. These compounds have served as scaffolds with the ability to attenuate Ca(2+) overload and excitotoxicity through several pathways. In this study, our focus was on mitigating Ca(2+) overload through the L-type calcium channels (LTCC). Here, we report the synthesis and biological evaluation of several novel polycyclic compounds. We determined the IC50 values for both the pentacycloundecylamines and the triquinylamines by means of a high-throughput fluorescence calcium flux assay utilizing Fura-2/AM. The potential of these compounds to offer protection against hydrogen peroxide-induced cell death was also evaluated. Overall, 8-benzylamino-8,11-oxapentacyclo[5.4.0.0(2,6) .0(3,10) .0(5,9) ]undecane (NGP1-01, 7a) had the most favorable pharmacological profile with an IC50 value of 86 µM for LTCC inhibition and significant reduction of hydrogen peroxide-induced cell death. In general, the triquinylamines were more active as LTCC blockers than the oxa-pentacycloundecylamines. The aza-pentacycloundecylamines were potent LTCC inhibitors, with 8-hydroxy-N-phenylethyl-8,11-azapentacyclo[5.4.0.0(2,6) .0(3,10) .0(5,9) ]undecane (8b) also able to offer significant protection in the cell viability assays.

Comonomer-induced stereo-selectivity enhancement in a c2 -symmetric metallocene-catalyzed propylene polymerization.

Propylene polymerization is carried out with a C 2 -symmetric metallocene catalyst of rac-Et(Ind)2 ZrCl2 /MAO at 40 °C in the presence of a cyclo-triene of trans,trans,cis-1,5,9-cyclododecatriene ((E,E,Z)-CDT). Comonomer incorporations are rather low (<0.10 mol%). However, it is shown for the first time that the comonomer causes a noticeable increase in poly-propylene -isotacticity (>7% in [mmmm]). (E,E,Z)-CDT is speculated to coordinate to the metal center forming comonomer-complexed active sites in charge of the entire polymerization reaction with decreased activity however increased propylene -enantiomorphic selectivity.

From Cassyrane to cashmeran - the molecular parameters of odorants.

This review, including some new experimental results, is the summary of a talk at the 'flavors & fragrances 2013' conference in Leipzig, organized jointly by the GDCh, the Liebig-Vereinigung, and the EuCheMS. After times of searching for natural odor principles and serendipitous discoveries by chemical inspiration, directed odorant design today offers the highest hit rates for the discovery of new odorants, although serendipity still plays a role. Keeping intact the electronic shape required for a certain olfactophore-binding geometry, one can add or subtract structural elements, rigidify molecular structures, or introduce more structural flexibility. To find out which structural features are critical, the 'seco-approach', in which different fragments are removed by cutting strategic bonds, is the most analytical. Following this approach, such ingredients as Serenolide, Sylkolide, and Pomarose were designed. Transferring this design principle from the family of damascones to that of the theaspiranes led to the discovery of Cassyrane, though completely different structural features turned out to be relevant. Application of the seco-concept to a 3,7a-substituted 2,6,7,7a-tetrahydro-1H-inden-5-yl musk lead structure derived from carotol resulted in the discovery of a new family of dienone musks with novel structure-odor correlations. However, cutting the C(2)-O bond of Cassyrane and oxidizing the resulting seco-structure to the 1,2,5,1″-tetradehydro derivative links the family of dienone musks with that of blackcurrant odorants, but the resulting target structures turned out to be potent orris odorants. (3E,5E)-5-(tert-Butyl)octadeca-3,5-dien-2-one even possesses the lowest odor threshold in the whole ionone family (0.036 ng/l air), which could be rationalized by a superposition analysis on (-)-cis-γ-irone. In the course of the synthesis of these high-impact orris odorants, we discovered that, depending on the reaction conditions, the dehydration step of the intermediate 5-hydroxyalk-3-yn-2-ones was accompanied by a carbenium-ion rearrangement. Depending on the substitution pattern, these rearrangement products and their derivatives possessed interesting musky-woody olfactory properties reminiscent of Cashmeran, demonstrating that the same structural elements can code for completely different odors, i.e., cassis, musk, orris, violet, and Cashmeran-type, depending only on their spatial arrangement.

Donor- and/or acceptor-substituted expanded radialenes: theory, synthesis, and properties.

The synthesis of donor- (D) and/or acceptor (A)-expanded [4]radialenes has been developed on the basis of readily available dibromoolefin (7), tetraethynylethene (10 and 20), and vinyl triflate (12) building blocks. The successful formation of D/A radialenes relies especially on (1) effective use of a series alkynyl protecting groups, (2) Sonogashira cross-coupling reactions, and (3) the development of ring closing reactions to form the desired macrocyclic products. The expanded [4]radialene products have been investigated by spectroscopic (UV-vis absorption and emission) and quantum chemical computational methods (density functional theory and time dependent DFT). The combined use of theory and experiment provides a basis to evaluate the extent of D/A interactions via the cross-conjugated radialene framework as well as an interpretation of the origin of D/A interactions at an orbital level.

Toward lead-oriented synthesis: one-pot version of Castagnoli condensation with nonactivated alicyclic anhydrides.

One-pot variation of Castagnoli condensation, that is, reaction of cyclic anhydrides, amines, and aldehydes, has been developed as a combinatorial approach to 1,2-disubstituted 5-oxopyrrolidine- and 6-oxopiperidine-3-carboxylic acids, as well as their benzo-analogues. Utility of the method to multigram preparation of building blocks and synthetic intermediates was also demonstrated. The final products are obtained in high yields and diastereoselectivity. The method fits well in the concept of lead-oriented synthesis; in particular, it can be used for the design of lead-like compound libraries, even if the strictest cut-offs are applied to the physicochemical properties of their members.

E pluribus unum: isolation, structure determination, network analysis and DFT studies of a single metastable structure from a shapeshifting mixture of 852 bullvalene structural isomers.

Bullvalene is an organic molecule that spontaneously undergoes Cope rearrangements, resulting in a reconfiguration of its carbon framework. During our study of oligosubstituted bullvalenes, which are structurally dynamic shapeshifting molecules, we found that we could isolate one metastable isomer from the interconverting population of 1680 constitutional isomers (852 structures if enantiomeric pairs are counted once). The preferential formation and unexpected stability of this isomer led to many questions, which we have addressed in this report. (1) What is its structure? (2) How many rearrangements are required to form this isomer from the initial bullvalene structure? (3) Why is it the preferred isomer? (4) What is the role of the substituents in its energetic preference? Our answers required synthesis, HPLC isolation, NMR characterizations, network construction and analysis, and computational (DFT) studies. The results of these efforts revealed the remarkable interconversion network of bullvalene rearrangements. The formation of this metastable isomer is preferred by both thermodynamic and kinetic factors and the ester substituent amplifies the energy difference between various structural isomers of oligosubstituted bullvalenes. The shapeshifting nature of oligosubstituted bullvalene is a useful and unusual property that has many potential applications. Insights into their rearrangements, energy landscape and substituent effect will be important knowledge for the development of these molecules towards materials, sensors and biologically active compounds.

Stereoselective α-quaternization of 3-methoxycycloalk-2-enones via 1,4-diastereoinduction of alkoxy dienolates.

The alkylation of dienolates generated from 3-methoxycycloalk-2-enones having a 3'-hydroxyl alkenyl chain provides the corresponding quaternized cycloalkenones in a highly diastereoselective manner. The high degree of stereocontrol in the α-quaternization possibly implies intervention of a rigid chelating transition state that allows an efficient 1,4-asymmetric induction to take place.

Ring-expansion metathesis polymerization: catalyst-dependent polymerization profiles.

Ring-expansion metathesis polymerization (REMP) mediated by recently developed cyclic Ru catalysts has been studied in detail with a focus on the polymer products obtained under varied reaction conditions and catalyst architectures. Depending upon the nature of the catalyst structure, two distinct molecular weight evolutions were observed. Polymerization conducted with catalysts bearing six-carbon tethers displayed rapid polymer molecular weight growth which reached a maximum value at ca. 70% monomer conversion, resembling a chain-growth polymerization mechanism. In contrast, five-carbon-tethered catalysts led to molecular weight growth that resembled a step-growth mechanism with a steep increase occurring only after 95% monomer conversion. The underlying reason for these mechanistic differences appeared to be ready release of five-carbon-tethered catalysts from growing polymer rings, which competed significantly with propagation. Owing to reversible chain transfer and the lack of end groups in REMP, the final molecular weights of cyclic polymers was controlled by thermodynamic equilibria. Large ring sizes in the range of 60-120 kDa were observed at equilibrium for polycyclooctene and polycyclododecatriene, which were found to be independent of catalyst structure and initial monomer/catalyst ratio. While six-carbon-tethered catalysts were slowly incorporated into the formed cyclic polymer, the incorporation of five-carbon-tethered catalysts was minimal, as revealed by ICP-MS. Further polymer analysis was conducted using melt-state magic-angle spinning (13)C NMR spectroscopy of both linear and cyclic polymers, which revealed little or no chain ends for the latter topology.

The influence of the solvent on the epoxidation of cis,trans,trans-1,5,9-cyclododecatriene to trans-1,2-epoxy-cis,trans-5,9-cyclododecadiene by catalytic system tert-butyl hydroperoxide/Mo(CO)6.

The epoxidation of cis,trans,trans-1,5,9-cyclododecatriene to trans-1,2-epoxy- cis,trans-5,9-cyclododecadiene with the use of commercial solution of tert-butyl hydroperoxide in various organic solvents: tert-butyl peroxide, isooctane, decane, and nonane was investigated. The process was investigated in different experimental conditions. The best results were achieved with the application of tert-butyl hydroperoxide in isooctane. A significant influence of the nature of the solvent on the results of trans-1,2-epoxy-cis,trans-5,9-cyclododecadiene synthesis was found.

New alicyclic musks: the fourth generation of musk odorants.

Musk odorants are one of the most important classes of fragrances in perfumery because they impart sensuality to perfume-oil compositions. Among the three well-known classes of musks, a new and very exciting generation of musk odorants, the so-called alicyclic musks, was discovered recently, of which Helvetolide (2) and Romandolide (3) are the most popular representatives so far. To find new, structurally related alicyclic musks, we have synthesized a library of 114 unique alicyclic molecules with modified cyclohexyl moieties. The olfactory properties of all compounds were evaluated to identify the structural requirements to be met for a musk odorant.

Transcellular signalling pathways and TNF-alpha release involved in formation of reactive oxygen species in rat alveolar macrophages exposed to tert-butylcyclohexane.

In the present work, the effects of aliphatic ( n-nonane and n-decane), alicyclic (1,2,4-trimethylcyclohexane and tert-butylcyclohexane, t-BCH) and aromatic (trimethylbenzene and tert-butylbenzene) hydrocarbon solvents on formation of reactive oxygen species (ROS) and the proinflammatory cytokine TNF-alpha in rat alveolar macrophages (AM) have been investigated. Formation of ROS was assessed by monitoring oxidation of 2',7'-dichlorofluorescin to 2',7'-dichlorofluorescein (DCF), and the proinflammatory cytokine tumour necrosis factor alpha (TNF-alpha) was detected using an enzyme-linked immunosorbent assay. DCF fluorescence was elevated in a concentration-dependent manner by the alicyclic hydrocarbons. The involvement of transcellular signalling pathways in the production of ROS by t-BCH, the most active compound, was elucidated by use of specific inhibitors. Preincubation of the AM with the mitogen-activated protein kinase (ERK 1/2) inhibitor U0126, the protein kinase C inhibitor bisindolylmaleimide, the superoxide dismutase inhibitor diethyldithiocarbamate, and the iron ion chelating agent deferoxamine reduced the DCF fluorescence significantly. t-BCH gave an increase in TNF-alpha release. Further, nitric oxide production measured by a modified Griess method, and intracellular calcium concentration measured by fura-2, were increased in the rat AM after exposure to t-BCH.

Highly enantioselective hydrolysis of alicyclic meso-epoxides with a bacterial epoxide hydrolase from Sphingomonas sp. HXN-200: simple syntheses of alicyclic vicinal trans-diols.

Hydrolysis of N-benzyloxycarbonyl-3,4-epoxy-pyrrolidine and cyclohexene oxide with the epoxide hydrolase of Sphingomonas sp. HXN-200, respectively, gave the corresponding vicinal trans-diols in high ee and yield, representing the first example of enantioselective hydrolysis of a meso-epoxide with a bacterial epoxide hydrolase.

Importance of the methyl group at C10 of squalene for hopene biosynthesis and novel carbocyclic skeletons with 6/5 + 5/5 + (6) ring system(s).

[reaction: see text] Incubation of (6E,10E,14E,18E)-2,6,10,19,23-pentamethyl-tetracosa-2,6,10,14,18,22-hexaene with Alicyclobacillus acidocaldarius hopene cyclase afforded four products having two types of carbocyclic skeletons, i.e., two hopane products and two products having an unprecedented carbocyclic skeleton of 6/5 + 5/5 +6 pentacyclic and 6/5 + 5/5 tetracyclic ring systems. The former two hopane skeletons were formed from the bioconversion of C15-desmethylsqualene and the latter two skeletons from that of C10-desmethylsqualene.

A systematic SAR study of C10 modified paclitaxel analogues using a combinatorial approach.

A library with 63 paclitaxel analogues modified at the C10 position of paclitaxel has been prepared using parallel solution phase synthesis. Most of the C10 analogues were slightly less active than paclitaxel in the tubulin assembly assay and had reduced potency in the B16 melanoma and MCF-7 cell line cytotoxicity assays. These modifications at C10, however, did not lead to the total loss of activity, indicating that the C10 moiety of paclitaxel may not be directly involved in the drug-microtubule interactions, but could influence its binding affinity to P-glycoprotein. Approximately 50% of the analogues demonstrated better activity against the drug resistant cell line MCF7-ADR. However, the increase in activity was 10-fold at most. This result demonstrates that the cytotoxicity against this drug resistant cancer cell line is sensitive to structural changes at the C10 position of paclitaxel. It was also found that the presence of a nitrogen atom in the C10 substituent might play a role in the interaction of analogues with microtubules.

The latest progress in the synthesis of carbocyclic nucleosides.

This review presents the latest developments in the field of carba-nucleosides (1994-1998). Special attention is paid to the synthesis of key precursors to those carba-nucleosides that possess significant biological activities or have novel structures.