Synthesis and DNA interaction of a mixed proflavine-phenanthroline Tröger base

Substrate Switchable Pathway for Selective Construction of Bridged Dibenzo[b,f][1,5]diazocines and Bridged Spiromethanodibenzo[b,e]azepines

An operationally simple method for the synthesis of bridged dibenzo[b,f][1,5]diazocines and bridged spiromethanodibenzo[b,e]azepines exhibiting bridged eight-membered and seven-membered molecular architecture is reported. This unique approach is based on substrate selective mechanistic pathway, including an unprecendented aerial oxidation-driven mechanism for the synthesis of bridged spiromethanodibenzo[b,e]azepines. The reaction is highly atom economic, and in addition, it allows the construction of two rings and four bonds in a single operation under metal-free condition. The easy availability of β enaminone and ortho phathalaldehyde as starting materials and the simple operation make this approach suitable for the preparation of important dibenzo[b,f][1,5]diazocine and spiromethanodibenzo[b,e]azepine cores.

Base-Catalyzed, Solvent-Free Synthesis of Rigid V-Shaped Epoxydibenzo[b,f][1,5]diazocines

A novel method for the synthesis of epoxydibenzo[b,f][1,5]diazocines exhibiting a V-shaped molecular architecture is reported. The unique approach is based on unprecedented base-catalyzed, solvent-free autocondensation and cross-condensation of fluorinated o-aminophenones. The structure of the newly synthesized diazocines was confirmed independently by X-ray analysis and chiroptical methods. The rigidity of the diazocine scaffold allowed for the separation of the racemate into single enantiomers that proved to be thermally stable up to 140 °C. Furthermore, the inertness of the diazocine scaffold was demonstrated by performing a series of typical transformations, including transition metal-catalyzed reactions, proceeding without affecting the bis-hemiaminal subunit.

Synthesis and Characterization of Macrocyclic Chiral Tröger's Base Phenhomazine Candidates as Anticancer Agent

1,4,7,10-Tetraoxa[10](2,8)trögerophane 5 was synthesized from its corresponding precursors. Heating of 2 with p-nitrophenoxide afforded bis(p-nitrophenyl)ether 3, which was treated with hydrazine hydrate to give bis(p-aminophenyl)ether 4. Treatment of 4 with paraformaldehyde and triflouroacetic anhydride gave trögerophane 5. Reaction of 5 with trifluroacetic anhydride afforded phenhomazine derivative 6, which was treated with potassium carbonate to afford tetrahydrophenhomazine 7. Finally, reaction of 7 with phenacylchloride, bromoacetic acid, or ethyl bromoacetate in the presence of triethyl amine under reflux, afforded the corresponding macrocyclic compounds 8, 9 and 10, respectively. The synthesized trögerophane,precursors and its newly synthesized phenhomazines derivatives were screened for anticancer activity. Results revealed that 1,4,7,10-tetraoxa[10](2,8)trögerophane had a promising selectivity towards colon cancer cell line with an IC₅₀ of 92.7 µg/ml.

Cooperation of copper and dioxygen for the site-selective construction of benzo[1,5]diazocin-6(5H)-ones from indoles and enaminone analogues

A new route for the preparation of benzo[1,5]diazocines from indoles and enaminone analogues is described.

Experimental and theoretical investigations into the stability of cyclic aminals

Background: Cyclic aminals are core features of natural products, drug molecules and important synthetic intermediates. Despite their relevance, systematic investigations into their stability towards hydrolysis depending on the pH value are lacking. Results: A set of cyclic aminals was synthesized and their stability quantified by kinetic measurements. Steric and electronic effects were investigated by choosing appropriate groups. Both molecular mechanics (MM) and density functional theory (DFT) based studies were applied to support and explain the results obtained. Rapid decomposition is observed in acidic aqueous media for all cyclic aminals which occurs as a reversible reaction. Electronic effects do not seem relevant with regard to stability, but the magnitude of the conformational energy of the ring system and pKa values of the N-3 nitrogen atom. Conclusion: Cyclic aminals are stable compounds when not exposed to acidic media and their stability is mainly dependent on the conformational energy of the ring system. Therefore, for the preparation and work-up of these valuable synthetic intermediates and natural products, appropriate conditions have to be chosen and for application as drug molecules their sensitivity towards hydrolysis has to be taken into account.

Synthesis of 6,12-Epiminodibenzo[b,f][1,5]diazocines via an Ytterbium Triflate-Catalyzed, AB2 Three-Component Reaction

An efficient and selective procedure for the synthesis of epiminodibenzo[b,f][1,5]diazocines involving a AB₂ three-component reaction is developed. Two equivalents of suitably substituted 2-aminoarylaldehydes reacted with arylamines in the presence of Yb(OTf)₃ to afford the desired products in high yields. The reaction is highly atom-economic and waste-free, in addition to allowing the generation of two heterocyclic rings and four C-N bonds in a single operation. Significantly, this approach is complementary to the existing literature procedures, affording arylamine-derived products that could not be accessed previously. A plausible mechanism is proposed involving an imine formation-intermolecular annulation-intramolecular iminium ion cyclization sequence.

Crystal structure of 1,1′-diformyl-4,4′-(6H,12H-5,11-methano-dibenzo[b,f][11,5]diazocine-2,8-diyl)dibenzene, C29H22N2O2

C29H22N2O2, triclinic, P1̅ (no. 2), a = 22.4995(6) Å, b = 9.9370(3) Å, c = 21.6466(6) Å, β = 115.941(1)°, V = 4352.1(2) Å3, Z = 4, R gt (F) = 0.0487, wR ref (F 2 ) = 0.1473, T = 296 K.

CuI-catalyzed amination of Tröger's base halides: a convenient method for synthesis of unsymmetrical Tröger's bases

A convenient and efficient Ullmann type copper catalyzed amination method has been developed for direct amination of halogen substituted Tröger's base analogues.

Synthesis and deposition of a Tröger’s base polymer on the electrode surface for potentiometric detection of a neuroblastoma tumor marker metabolite

We propose an innovative approach to detect a low molecular weight metabolite of neuroblastoma.

Synthesis and biological activity evaluation of hydrazone derivatives based on a Tröger's base skeleton

We report the design and synthesis of novel anticancer agents based on bis-hydrazones separated by a rigid Tröger's base skeleton. This novel approach combines a biologically active moiety (hydrazone) with this scaffold (Tröger's base) to construct DNA intercalators. Evaluation of the anticancer activity of these agents using seven cancer cell lines and two healthy cell lines found that several derivatives had potent anticancer activity and excellent selectivity indexes toward cancer cells. The antimicrobial activities were tested on a set of thirteen bacterial stains, but the prepared compounds were not active. Complexation studies using biologically important metal ions demonstrated that these compounds are able to bind Cu(2+), Fe(3+), Co(2+), Ni(2+) and Zn(2+). DNA intercalation studies showed that the compounds themselves do not interact with DNA, but their metallocomplexes do interact, most likely via intercalation into DNA.

Photophysical characterisation of Tröger's base molecular scaffolds: a combined theoretical and experimental study

The photophysics of Tröger's base in the ground and excited states was performed by comparing experimental and theoretical properties predicted using TD-DFT calculations.

Discovery of Tröger's base analogues as selective inhibitors against human breast cancer cell line: design, synthesis and cytotoxic evaluation

A library of structurally diverse Tröger's base analogues has been constructed via unusual amination of methylene bridge employing Vilsmeier-Haack conditions as well as by the incorporation of five and six membered heterocycles on the aromatic core of Tröger's base framework. The constructed structurally diverse frameworks were evaluated for their cytotoxic activities against a panel of three human cancer lines A549 (lung adenocarcinoma), MDAMB-231 (breast) and SK-N-SH (neuroblastoma). From the activity profile obtained, a redesign of Tröger's base analogues led to the construction of more potent molecular entities. The study led to development of a series of compounds with MDAMB-231 cell line specific cytotoxicity. Of the 30 compounds synthesized and evaluated, 7 compounds were found to possess cytotoxicity that is equivalent or better than standard drug doxorubicin against MDAMB-231 cell line while only one compound was found to be active against SK-N-SH cell line.

Stabilization and structural alteration of the G-quadruplex DNA made from the human telomeric repeat mediated by Tröger's base based novel benzimidazole derivatives

Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Tröger's base skeleton with the G-quadruplex DNA (G4DNA). These Tröger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.

Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode

Despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform self-dockings and cross dockings between two DNA ligands (a minor groove binder and an intercalator) and four distinct receptors: 1) crystallographic DNA without intercalation gap; 2) crystallographic DNA with intercalation gap; 3) canonical B-DNA; and 4) modified B-DNA with intercalation gap. Besides being efficient in self-dockings, AutoDock is capable of correctly identifying two of the main DNA binding modes with the condition that the target possesses an artificial intercalation gap. Therefore, we suggest a default protocol to identify DNA binding modes which uses a modified canonical DNA (with gap) as receptor. This protocol was applied to dock two different Troger bases to DNA and the predicted binding modes agree with those suggested, yet not established, by experimental data. We also applied the protocol to dock aflatoxin B(1) exo-8,9-epoxide, and the results are in complete agreement with experimental data from the literature. We propose that this approach can be used to investigate other ligands whose binding mode to DNA remains unknown, yielding a suitable starting point for further theoretical studies such as molecular dynamics simulations.

Optically active Ru(II) complexes with a chiral Tröger’s base ligand and their interactions with DNA

Three stereoisomers of a Ru(II) complex bearing a chiral bis-phenanthroline Tröger's base analogue, TBphen2 (1), have been isolated from the reaction of the enantiomerically pure precursor complex Lambda- (or Delta-) cis-[Ru(phen)2(py)2]2+ (phen=1,10-phenanthroline, py=pyridine) with the racemic mixture of 1. Each stereoisomer of [Ru(phen)2TBphen2]2+ (2) has been characterized by 1H NMR and CD spectroscopy. Electrochemical studies revealed that the redox properties of 2 are not influenced by the stereochemistry, however, the electrochemical oxidation of the metallic center is irreversible because of the diazocine bridge of the TBphen2 ligand. Steady-state emission measurements in the presence of calf thymus DNA showed that the DNA binding of [Ru(phen)2TBphen2]2+ depends on the stereoisomer and is mainly controlled by the absolute configuration of the metal center of the complex. The affinity constant for the stereoisomer Delta-S-2 is 10(2) higher than that for Lambda-S-2 and rac-[Ru(phen)3]2+.

The Mechanism of Tröger's Base Formation Probed by Electrospray Ionization Mass Spectrometry

Using direct infusion electrospray ionization mass and tandem mass spectrometric experiments [ESI-MS(/MS)], we have performed on-line monitoring of some reactions used to form Tröger's bases. Key intermediates, either as cationic species or as protonated forms of neutral species, have been intercepted and characterized. The role of urotropine as the methylene source in these reactions has also been accessed. Reaction pathways shown by ESI-MS(/MS) have been probed by gas-phase ion/molecule reactions, and an expanded mechanism for Tröger's base formation based on the mass spectrometric data has been elaborated.

A New Bis-Tröger's Base: Synthesis, Spectroscopy, Crystal Structure and Isomerization

A new bis-Tröger's base was prepared from a tetraamine precursor as a mixture of two diastereoisomers. One of the isomers has a chair-like geometry, and the other possesses a boat-like geometry, embodying molecular tweezers. A one-pot preparation of bis-TB isomers and their interconversion under acid conditions was also studied. Structures of both isomers were confirmed by single-crystal X-ray diffraction. Extensive spectroscopic data, including 1H and 13C NMR, IR and Raman spectra of the isomers, are given.

Synthetic Routes to Linear Oligo-Tröger's Bases

Derivatives of Tröger's base (TB) have played important roles in receptor construction due to their rigid V-shape. A new class of these compounds are the oligo-TBs, which can function as cavitands. Herein, we describe both stepwise and one-step (oligomerization) methods suitable for the preparation of linear oligo-TBs.