9-Azahomocubane.

Homocubane, a highly strained cage hydrocarbon, contains two very different positions for the introduction of a nitrogen atom into the skeleton, e. g., a position 1 exchange results in a tertiary amine whereas position 9 yields a secondary amine. Herein reported is the synthesis of 9-azahomocubane along with associated structural characterization, physical property analysis and chemical reactivity. Not only is 9-azahomocubane readily synthesized, and found to be stable as predicted, the basicity of the secondary amine was observed to be significantly lower than the structurally related azabicyclo[2.2.1]heptane, although similar to 1-azahomocubane.

seco-1-Azacubane-2-carboxylic Acid: Derivative Scope and Comparative Biological Evaluation.

The unusual and sterically constrained amino acid, seco-1-azacubane-2-carboxylic acid, was incorporated into a range of bioactive chemical templates, including enalaprilat, perindoprilat, endomorphin-2 and isoniazid, and subjected to biological testing. The endomorphin-2 derivative displayed increased activity at the δ opioid receptor, but a loss in activity was observed in the other cases, although human normal cell line evaluation suggests limited cytotoxic effects.

seco-1-Azacubane-2-carboxylic acid-Amide Bond Comparison to Proline.

seco-1-Azacubane-2-carboxylic acid, an unusual and sterically constrained amino acid, was found to undergo amide bond formation at both the N- and C-termini using proline based bioactive molecule templates as a concept platform.

Cage hydrocarbons as linkers in dimeric drug design: Case studies with trimethoprim and tedizolid.

The looming threat of a "post-antibiotic era" has been caused by a rapid rise in antibacterial resistance and subsequent depletion of effective antibiotic agents in the clinic. An efficient strategy to address this shortfall lies in the reengineering of pre-existing and commercially available antibiotic drugs. This is exemplified by dimerization, a design concept in which two pharmacophores are covalently linked to form a new chemical entity. The cage hydrocarbons cubane (1), bicyclo[2.2.2]octane (BCO) (2), adamantane (3), and bicyclo[1.1.1]pentane (BCP) (4) present themselves as an attractive family of linkers in this regard. In this report, all four hydrocarbon cages were employed as linkers in a series of dimers based on the commercially available antibiotics trimethoprim and tedizolid. A detailed synthetic roadmap for the protection and deprotection of each pharmacophore is outlined. Several members of the trimethoprim series showed activity on par with that of their trimethoprim progenitor, although this was not the case for the tedizolid series. The design strategy outlined herein highlights the utility of the group as a platform for the rapid and modular construction of future novel antibiotics.

Comprehensive Computational Investigation of the Barton-Kellogg Reaction for Both Alkyl and Aryl Systems.

The course of the Barton-Kellogg (BK) reaction for alkyl- and aryl-substituted substrates has been investigated at the DLPNO-CCSD(T)/def2-TZVPP//ωB97X-D/def2-TZVPP level of theory, with results compared to available experimental kinetic data. Through comparison with the unsubstituted parent system, the preference for the formation of 1,3,4-dihydrothiadiazole over the isomeric 1,2,3-dihydrothiadiazole was observed to result from reduced steric repulsion in the relevant transition-state structure. Nitrogen extrusion [retro-(3 + 2)-cycloaddition] from the intermediate dihydrothiadiazole was found to be the rate-determining step. The barrier for this process was, however, significantly lower for aromatic substrates, which is consistent with the difficulty in isolating aryl-substituted dihydrothiadiazoles. The electronic structure of the transient thiocarbonyl ylide was also investigated, highlighting the contradictory results from wave-function theory- and density functional theory-based methods. Correlation of unrestricted natural orbital eigenvalues with previous experimental models suggested that the dipole intermediates possess low diradical character and are therefore considered to be closed-shell species. Exergonic conrotatory electrocyclization of the dipole led to sterically congested thiirane products, even for very bulky systems (di-t-butyl). These results complement the recent work of Mloston et al. Finally, DLPNO-CCSD(T)//ωB97X-D was found to be a reliable method for estimating the feasibility of the BK reaction, which should assist experimentalists in the selection of viable substrates.

GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans.

Glycosaminoglycans (GAGs) are a family of anionic carbohydrates that play an essential role in the physiology and pathology of all eukaryotic life forms. Experimental determination of GAG-protein complexes is challenging due to their difficult isolation from biological sources, natural heterogeneity, and conformational flexibility-including possible ring puckering of sulfated iduronic acid from 1C4 to 2SO conformation. To overcome these challenges, we present GlycoTorch Vina (GTV), a molecular docking tool based on the carbohydrate docking program VinaCarb (VC). Our program is unique in that it contains parameters to model 2SO sugars while also supporting glycosidic linkages specific to GAGs. We discuss how crystallographic models of carbohydrates can be biased by the choice of refinement software and structural dictionaries. To overcome these variations, we carefully curated 12 of the best available GAG and GAG-like crystal structures (ranging from tetra- to octasaccharides or longer) obtained from the PDB-REDO server and refined using the same protocol. Both GTV and VC produced pose predictions with a mean root-mean-square deviation (RMSD) of 3.1 Å from the native crystal structure-a statistically significant improvement when compared to AutoDock Vina (4.5 Å) and the commercial software Glide (5.9 Å). Examples of how real-space correlation coefficients can be used to better assess the accuracy of docking pose predictions are given. Comparisons between statistical distributions of empirical "salt bridge" interactions, relevant to GAGs, were compared to density functional theory (DFT) studies of model salt bridges, and water-mediated salt bridges; however, there was generally a poor agreement between these data. Water bridges appear to play an important, yet poorly understood, role in the structures of GAG-protein complexes. To aid in the rapid prototyping of future pose scoring functions, we include a module that allows users to include their own torsional and nonbonded parameters.

Synthesis of the seco-Limonoid BCD Ring System Identifies a Hsp90 Chaperon Machinery (p23) Inhibitor.

D-Ring-seco-limonoids (tetranortriterpenoids), such as gedunin and xylogranin B display anti-cancer activity, acting via inhibition of Hsp90 and/or associated chaperon machinery (e.g., p23). Despite this, these natural products have received relatively little attention, both in terms of an enabling synthetic approach (which would allow access to derivatives), and as a consequence their structure-activity relationship (SAR). Disclosed herein is a generally applicable synthetic route to the BCD ring system of the seco-D-ring double bond containing limonoids. Furthermore, cell based assays revealed the first skeletal fragment that exhibited inhibition of the p23 enzyme at a level which was equipotent to that of gedunin, despite being much less structurally complex.

Cyclooctatetraene: A Bioactive Cubane Paradigm Complement.

Cubane was recently validated as a phenyl ring (bio)isostere, but highly strained caged carbocyclic systems lack π character, which is often critical for mediating key biological interactions. This electronic property restriction associated with cubane has been addressed herein with cyclooctatetraene (COT), using known pharmaceutical and agrochemical compounds as templates. COT either outperformed or matched cubane in multiple cases suggesting that versatile complementarity exists between the two systems for enhanced bioactive molecule discovery.

Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopyrylium Ylides: The Significance of Molecular Orbital Isosymmetry.

By drawing analogies from the dimerization of cyclopentadiene, a novel reaction pathway bifurcation is uncovered in the cycloaddition of oxidopyrylium ylides and butadiene. Analysis of the potential energy surface (at the M06-2X/6-311+G(d,p) level of theory) in combination with Born-Oppenheimer molecular dynamics simulations (M06-2X/6-31+G(d)) demonstrate that both the (4 + 3)- and (5 + 2)-cycloaddition products are accessed from the same transition state. Key indicators of a pathway bifurcation (asynchronous bond formation, and a second transition state for the interconversion of the products) are also observed. The absence of a post-transition state bifurcation in the related oxidopyridinium systems of Krenske and Harmata is rationalized. Finally, the isosymmetry of the oxidopyrylium and cyclopentadiene molecular orbitals as well as the presence of "secondary orbital interactions" are emphasized as the common source of nonstatistical behavior. Application of these principles will allow for the rapid identification of new reaction pathway bifurcations.

The cubane paradigm in bioactive molecule discovery: further scope, limitations and the cyclooctatetraene complement.

The cubane phenyl ring bioisostere paradigm was further explored in an extensive study covering a wide range of pharmaceutical and agrochemical templates, which included antibiotics (cefaclor, penicillin G) and antihistamine (diphenhydramine), a smooth muscle relaxant (alverine), an anaesthetic (ketamine), an agrochemical instecticide (triflumuron), an antiparasitic (benznidazole) and an anticancer agent (tamibarotene). This investigation highlights the scope and limitations of incorporating cubane into bioactive molecule discovery, both in terms of synthetic compatibility and physical property matching. Cubane maintained bioisosterism in the case of the Chagas disease antiparasitic benznidazole, although it was less active in the case of the anticancer agent (tamibarotenne). Application of the cyclooctatetraene (COT) (bio)motif complement was found to optimize benznidazole relative to the benzene parent, and augmented anticancer activity relative to the cubane analogue in the case of tamibarotene. Like all bioisosteres, scaffolds and biomotifs, however, there are limitations (e.g. synthetic implementation), and these have been specifically highlighted herein using failed examples. A summary of all templates prepared to date by our group that were biologically evaluated strongly supports the concept that cubane is a valuable tool in bioactive molecule discovery and COT is a viable complement.

Computational evidence for a reaction pathway bifurcation in Sasaki-type (4 + 3)-cycloadditions.

The current report seeks to validate the existence of a post-transition state bifurcation in the Lewis acid-catalysed (4 + 3)-cycloaddition of butadiene and α-methoxy acrolein. Cycloaddition transition state (TS) structures are shown by intrinsic reaction coordinate (IRC) and potential energy surface (PES) scan calculations to connect directly to both (4 + 3)- and (4 + 2)-products. A second TS, a 1,2-sigmatropic shift which interconverts the products, was also located. Implicit solvent is observed to have a substantial effect of the course of the reaction, with the minimum energy path from the gas phase TS leading to (4 + 2)-product whereas the DCM solvent phase TS leads to (4 + 3)-product. On the basis of these data it is suggested that a number of previously reported (4 + 3)-cycloadditions may also possess reaction pathway bifurcations.

Claisen rearrangements of benzyl vinyl ethers: theoretical investigation of mechanism, substituent effects, and regioselectivity.

Recently we reported the aromatic Claisen rearrangements of benzyl ketene acetals, which form one of the few examples of aromatic Claisen rearrangements involving benzyl vinyl ethers (as opposed to allyl aryl ethers, which are the usual substrates for aromatic Claisen rearrangements). Theoretical calculations predict that these rearrangements proceed via a concerted [3,3]-sigmatropic transition state, which is similar in geometry to the TS for the Claisen rearrangement of an allyl aryl ether but has a 4 kcal mol-1 higher barrier. The effects of donor (OMe) and acceptor (CN) substituents on the kinetics of the [3,3]-rearrangement mirror those reported for allyl vinyl ethers: the largest substituent effects are seen for 1-OMe, 2-OMe, 2-CN, and 4-CN substituents, which lower the barrier by 5-9 kcal mol-1. Substituents on the aromatic ring have smaller effects on the barrier (≤2 kcal mol-1). The regioselectivities of Claisen rearrangements of meta-substituted benzyl ketene acetals favour 1,2,3-trisubstituted products in preference to the less sterically congested 1,2,4-isomers due to favourable orbital interactions in the 1,2,3 transition state.

1-Azahomocubane.

Highly strained cage hydrocarbons have long stood as fundamental molecules to explore the limits of chemical stability and reactivity, probe physical properties, and more recently as bioactive molecules and in materials discovery. Interestingly, the nitrogenous congeners have attracted much less attention. Previously absent from the literature, azahomocubanes, offer an opportunity to investigate the effects of a nitrogen atom when incorporated into a highly constrained polycyclic environment. Herein disclosed is the synthesis of 1-azahomocubane, accompanied by comprehensive structural characterization, physical property analysis and chemical reactivity. These data support the conclusion that nitrogen is remarkably well tolerated in a highly strained environment.

1,4-Diazacubane crystal structure rectified as piperazinium.

All 21 [n]-azacubanes are proposed by theoreticians to be stable, however, to-date only the synthesis of 1,4-diazacubane has been reported - as a Ni2+ templated Kagome metal organic framework (MOF). Described herein is the structural reassignment of this Kagome MOF on the basis of deducing the precise experimental procedure, and demonstrating that rather than the formation of 1,4-diazacubane, charge is balanced by disordered piperazinium cations across a twelve-fold symmetry site. Furthermore, quantum chemical calculations reveal that 1,4-diazacubane is unlikely to form under the reported conditions due to unfavorable enthalpies for select hypothetical reactions leading to such a product. This significant structure correction upholds the unconquered synthesis status quo of azacubane.