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.

Isolation and In Vitro and In Vivo Activity of Secondary Metabolites from Clerodendrum polycephalum Baker against Plasmodium Malaria Parasites.

Chemical investigation of the antimalarial medicinal plant Clerodendrum polycephalum led to the isolation of five new diterpenoids, including ajugarins VII-X (1-4) and teuvincenone K (5), along with four known compounds, namely, 12,16-epoxy-6,11,14,17-tetrahydroxy-17(15 → 16)-abeo-5,8,11,13,15-abietapentaen-7-one (6), methyl pheophorbide A (7), loliolide (8), and acacetin (9). The chemical structures of the new compounds were elucidated using NMR spectroscopy, mass spectrometry, circular dichroism, as well as density functional theory calculations. All compounds were evaluated for in vitro activity against Plasmodium falciparum 3D7 malaria parasites with methyl pheophorbide A (7) showing the strongest activity (IC50 4.49 µM). Subsequent in vivo testing in a Plasmodium berghei chemosuppression model showed that compound 7 significantly attenuated peripheral blood parasitemia, leading to 79% and 87% chemosuppression following oral doses at 10 and 20 mg/kg, respectively.

A New Metric for Evaluating DFT Calculated Proton and Carbon Chemical Shifts of Natural Products and Organic Compounds.

The calculation of DFT (density functional theory) chemical shifts have become an important technique for the verification of a proposed structure. An easily calculated metric developed for proton and carbon chemical shifts of natural products and organic compounds, the calculated chemical shift index (CCSI), has been developed, which uses the deviation of each pair of calculated and experimental chemical shifts. The mean absolute deviation (MAD), which is commonly used as the goodness of fit metric for DFT calculated chemical shifts, can conceal large deviations in the calculated data. A classification strategy is also proposed for the CCSI to highlight when further assessment of the NMR data is required.

Synthesis, isolation and characterisation of fluorinated-benzimidazoisoquinoline regioisomers.

A pair of novel fluorinated-benzimidazoisoquinoline regioisomers was synthesised and isolated. Initial structural characterisation and identification employed 1D proton, 1D carbon, correlated spectroscopy (COSY), heteronuclear single quantum coherence (HSQC), and heteronuclear multiple bond correlation (HMBC) nuclear magnetic resonance spectroscopy and mass spectrometry. However, the fluorinated regioisomers could not be differentiated using nuclear magnetic resonance (NMR) alone. Density functional theory calculations and single-crystal X-ray diffraction experiments were used to completely characterise and identify the compounds.

Synthetic Tigliane Intermediates Engage Thiols to Induce Potent Cell Line Selective Anti-Cancer Activity.

The tigliane ring system, which encompasses iconic members such as phorbol and TPA, is widely renowned due to numerous observations of displaying potent biological activity, and subsequent use as mainstream biochemical tools. Traditionally, naturally occurring phorboids are regarded as tumor promotors through PKC activation, although in recent times more highly oxidized natural derivatives have been identified as anti-tumor agents. In the view that only limited synthetic investigations toward skeletal stereochemical modification have been undertaken, non-natural systems could be useful for a better understanding of the tigliane pharmacophore via interrogation of cellular sensitivity. In this context the concise construction of a number of highly functionalized non-natural D-ring inverted phorbol esters were synthesized, via a rhodium-catalyzed [4+3] cycloaddition, and biologically evaluated using a range of cancer cell lines. The biological results highlight the notion that subtle changes in structure have dramatic effects on potency. Furthermore, although the non-natural derivatives did not outcompete the natural systems in the PKC-activation sensitive MCF7 cancer cell line, they outperformed in other cancer cell lines (MM96L and CAL27). This observation strongly suggested an alternate mode of action not involving activation of PKC, but instead involves thiol addition as indicated by glutathione addition and NF-κB reporter activity.

Chemical constituents from Macleaya cordata (Willd) R. Br. and their phenotypic functions against a Parkinson's disease patient-derived cell line.

Cytological profiling (CP) assay against a human olfactory neuroshpere-derived (hONS) cell line using a library of traditional Chinese medicinal plant extracts gave indications that the ethanolic extract of Macleaya cordata (Willd) R. Br. elicited strong perturbations to various cellular components. Further chemical investigation of this extract resulted in the isolation of two new benzo[c]phenanthridine alkaloids, (6R)-10-methoxybocconoline (1) and 6-(1-hydroxyethyl)-10-methoxy-5,6-dihydrochelerythrine (2). Their planar structures were elucidated by extensive 1D and 2D NMR studies, together with MS data. The absolute configuration for position C-6 of 1 and relative configurations for position C-6 and C-1' of 2 were assigned by density functional theory (DFT) calculations of ECD and NMR data, respectively. Also isolated were fourteen known metabolites, including ten alkaloids (3-12) and four coumaroyl-containing compounds (13-16). Cytological profiling of the isolates against Parkinson's Disease (PD) patient-derived olfactory cells revealed bocconoline (3) and 6-(1-hydroxyethyl)-5,6-dihydrochelerythrine (4) significantly perturbated the features of cellular organelles including early endosomes, mitochondria and autophagosomes. Given that hONS cells from PD patients model some functional aspects of the disease, the results suggested that these phenotypic profiles may have a role in the mechanisms underlying PD and signified the efficacy of CP in finding potential chemical tools to study the biological pathways in PD.

Dynamic NMR and Computational Studies Inform the Conformational Description of Dendrillane Terpenes from the Nudibranch Goniobranchus coi.

Two new oxygenated terpenes (1 and 2) have been characterized from the Australian nudibranch Goniobranchus coi. Broadened 1H NMR signals, together with the absence of individual carbon NMR signals, complicated analysis of 5,9-epoxydendrillolide A (1); increasing the temperature to 323 K revealed the missing NMR signals. Low-temperature 1H NMR experiments provided an activation barrier of ∼15 kcal mol-1 and, together with DFT calculations, supported interconversion of a twist chair conformer with two different chair conformers. X-ray crystallographic analysis coupled with biosynthetic reasoning suggested a (5R, 8S, 9R, 13R, 14R, 15R, 16R) configuration. Ketone 2 demonstrated similar dynamic conformational processes to 1.

Elucidation of Relative and Absolute Configurations of Highly Rearranged Diterpenoids and Evidence for a Putative Biosynthetic Intermediate from the Australian Nudibranch Goniobranchus geometricus.

A diterpene (1), previously isolated from a Japanese marine sponge, together with two undescribed (2, 3) diterpenes with highly rearranged carbon skeletons have been characterized from the Australian nudibranch species Goniobranchus geometricus. The structures and relative configuration were determined by spectroscopic analyses informed by detailed molecular modeling, as well as by DFT, DP4, and coupling constant predictions. A 13 R,14 R configuration was determined for secoshahamin (1) by chemical correlation with 12-desacetoxyshahamin C (4) and 12-desacetoxypolyrhaphin A (5); each metabolite (1, 4, and 5) was subjected to saponification and lactonization, yielding the same δ-lactone product (6). Secoshahamin has the same carbon skeleton as a putative precursor that may play a key role in the biosynthesis of highly rearranged diterpenoid scaffolds via C-9/C-11 cleavage of a spongian diterpene precursor.

Catalyst-Controlled Stereoselective Synthesis Secures the Structure of the Antimalarial Isocyanoterpene Pustulosaisonitrile-1.

Three new isocyanoditerpenes (5-7) have been characterized from Australian specimens of the nudibranch Phyllidiella pustulosa. The planar structure and (3R,6S,7R) absolute configuration of pustulosaisonitrile-1 were deduced by spectroscopic analyses at 900 MHz informed by molecular modeling, DFT calculations, and computational NMR chemical shift predictions and by comparison of experimental electronic circular dichroism (ECD) data with TDDFT-ECD calculations for the truncated model compound 8. A catalyst-controlled enantio- and diastereoselective total synthesis of the two most likely diastereomeric candidates for the structure of 5 solidified its (3R,6S,7R,10S,11R,14R) absolute configuration. Three individual enantioselective methods provided stereochemical control at key positions, permitting an unambiguous final structural assignment. Isocyanide 5 and synthetic diastereomers 5a and 5c showed activity against Plasmodium falciparum malaria parasites (IC50 ∼1 µM).

Antitubercular and Cytotoxic Chlorinated seco-Cyclohexenes from Uvaria alba.

Two new chlorine-containing polyoxygenated seco-cyclohexenes, albanols A (1) and B (2), along with the oxepinone metabolite grandiuvarone (3) were isolated from the endemic Philippine Annonaceae plant Uvaria alba. Both new compounds exhibited modest antitubercular activity. Compound 1 showed cytostatic activity (ranging from 1-50 µM) against HeLa cells and weak antiproliferative activity against HUVEC and K-562 cells with GI50 values of 106 and 81 µM, respectively.

Revision of the Structure of Acremine P from a Marine-Derived Strain of Acremonium persicinum.

The previously published structure of the fungal metabolite acremine P is revised by re-evaluation of chemical shift values and NOESY data, and by DFT calculations.

Rhodocomatulin-Type Anthraquinones from the Australian Marine Invertebrates Clathria hirsuta and Comatula rotalaria.

Chemical investigations of an Australian sponge, Clathria hirsuta, from the Great Barrier Reef, have resulted in the isolation of two known anthraquinones, rhodocomatulin 5,7-dimethyl ether (1) and rhodocomatulin 7-methyl ether (2). Additionally, four new anthraquinone metabolites, 6-methoxyrhodocomatulin 7-methyl ether, 3-bromo-6-methoxy-12-desethylrhodocomatulin 7-methyl ether, 3-bromo-6-methoxyrhodocomatulin 7-methyl ether, and 3-bromorhodocomatulin 7-methyl ether (3-6), were also isolated and characterized. This is the first report of the rhodocomatulin-type anthraquinones from a marine sponge, as 1 and 2 were previously isolated from the marine crinoid genus Comatula. An additional chemical investigation of the marine crinoid Comatula rotalaria enabled the isolation of further quantities of 1 and 2, as well as two additional new crinoid metabolites, 12-desethylrhodocomatulin 5,7-dimethyl ether and 12-desethylrhodocomatulin 7-methyl ether (7 and 8). An NMR spectroscopic analysis of compounds 7 and 8 provided further insight into the rhodocomatulin planar structure and, together with the successful implementation of DFT-NMR calculations, confirmed that the rhodocomatulin metabolites existed as para rather than ortho quinones.

Rearranged Diterpenes and Norditerpenes from Three Australian Goniobranchus Mollusks.

Three new norditerpenes (1, 6, and 7) and four diterpenes (2-5) with extensively rearranged carbon skeletons have been characterized from Australian nudibranchs. The relative configuration of the cyclopropyl-containing verrielactone (1) from Goniobranchus verrieri was suggested by spectroscopic analysis at 500 MHz informed by a combination of molecular modeling and DFT calculations. The nudibranchs G. splendidus and G. cf. splendidus provided 2-7, for which the structures and stereochemistry were deduced by 2D NMR studies at either 500 or 700 MHz. Each of the seven terpenoids exhibited a carbon skeleton modified from one of the tetrahydroaplysulphurin, spongionellin, or gracilane series of terpenes. A biosynthetic pathway to terpenes 1-7 from spongialactone is proposed.

Investigation of two- and three-bond carbon-hydrogen coupling constants in cinnamic acid based compounds.

Two- and three-bond coupling constants (2 JHC and 3 JHC ) were determined for a series of 12 substituted cinnamic acids using a selective 2D inphase/antiphase (IPAP)-single quantum multiple bond correlation (HSQMBC) and 1D proton coupled 13 C NMR experiments. The coupling constants from two methods were compared and found to give very similar values. The results showed coupling constant values ranging from 1.7 to 9.7 Hz and 1.0 to 9.6 Hz for the IPAP-HSQMBC and the direct 13 C NMR experiments, respectively. The experimental values of the coupling constants were compared with discrete density functional theory (DFT) calculated values and were found to be in good agreement for the 3 JHC . However, the DFT method under estimated the 2 JHC coupling constants. Knowing the limitations of the measurement and calculation of these multibond coupling constants will add confidence to the assignment of conformation or stereochemical aspects of complex molecules like natural products. Copyright © 2016 John Wiley & Sons, Ltd.

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

Antimalarial Isocyano and Isothiocyanato Sesquiterpenes with Tri- and Bicyclic Skeletons from the Nudibranch Phyllidia ocellata.

Five new isocyano/isothiocyanato sesquiterpenes (1-5) with tri- or bicyclic carbon skeletons have been characterized from Australian specimens of the nudibranch Phyllidia ocellata. Spectroscopic analyses at 900 MHz were informed by DFT calculations. The 1S, 5S, 8R configuration of 2-isocyanoclovene (1) was determined by X-ray crystallographic analysis of formamide 6. A biosynthetic pathway to clovanes 1 and 2 from epicaryolane precursors is proposed. Isocyanides 1, 2, and 4 showed activity against Plasmodium falciparum (IC50 0.26-0.30 µM), while isothiocyanate 3 and formamide 6 had IC50 values of >10 µM.

1H and 13C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory.

Calculation of NMR chemical shifts and coupling constants using quantum mechanical calculations [density functional theory (DFT)], has become a very popular tool for the determination of conformation and the assignment of stereochemistry within a molecule. We present the scaling factors (linear regression parameters) from 10 DFT methods for 10 commonly used NMR solvents using the same set of reference compounds. The results were compared with the corresponding gas-phase calculations to assess the inclusion of the polarizable continuum model for solvent effects.

Synthesis, NMR structural characterization and molecular modeling of substituted thiosemicarbazones and semicarbazones using DFT calculations to prove the syn/anti isomer formation.

Thiosemicarbazones possessing electron-donating and electron-withdrawing groups were prepared, and their spectral characteristics determined. In all cases, the spectra showed that one isomer was formed, allowing further functionalization to molecules of biological interest. We provide NMR data for some of the thiosemicarbazones and semicarbazones. We also provide evidence that for 2-pyridyl thiosemicarbazone, the syn isomer slowly converts into the anti isomer in dimethyl sulfoxide solvent with first-order kinetics. Molecular modeling and density functional theory calculations confirmed these observations.