Synthesis, cytotoxicity, QSAR, and intercalation study of new diindenopyridine derivatives

Di-indenopyridines as topoisomerase II-selective anticancer agents: Design, synthesis, and structure-activity relationships

Topoisomerases are key molecular enzymes responsible for altering DNA topology, thus they have long been considered as attractive targets for novel chemotherapeutic agents. Topoisomerase type II (Topo II) catalytic inhibitors embrace a fresh perspective meant to get beyond drawbacks caused by topo II poisons, such as cardiotoxicity and secondary malignancies. Based on previously reported 5H-indeno[1,2-b]pyridines, here we presented new twenty-three hybrid di-indenopyridines along with their topo I/IIα inhibitory and antiproliferative activity. Most of the prepared 11-phenyl-diindenopyridines showed negligible topo I inhibitory activity, showing selectivity over topo II. Among the series, we finally selected compound 17, which displayed 100 % topo IIα inhibition at 20 μM concentration and comparable antiproliferative activity against the tested cell lines. Through competitive EtBr displacement assay, cleavable complex assay, and comet assay, compound 17 was finally determined as a non-intercalative catalytic topo IIα inhibitor. The findings in this study highlight the significance of phenolic, halophenyl, thienyl, and furyl groups at the 4-position of the indane ring in the design and synthesis of di-indenopyridines as potent catalytic topo IIα inhibitors with remarkable anticancer effects.

Development of oxoisoaporphine derivatives with topoisomerase I inhibition and reversal of multidrug resistance in breast cancer MCF-7/ADR cells

A series of oxoisoaporphine derivatives with topoisomerase I inhibition and cytotoxic activities. Among them, compound 14 showed the most potent cytotoxic activity against all cancer cell lines tested, and substantially lower cytotoxicity to LO2 cells. Molecular docking studies, dynamics simulation and a follow-up enzyme inhibition assay indicated that 14 could interfere with DNA and significantly inhibit the activity of topoisomerase I. Further mechanistic studies revealed that 14 could arrest cell cycle at the G1 phase, and finally killed MCF-7 cells via apoptosis. In addition, 14 exhibited remarkable chemoreversal ability on multidrug-resistant MCF-7/ADR breast cancer cells. Some of its mechanisms may be related to inhibition of MCF-7/ADR P-gp-mediated Rhodamine (Rh123) efflux function and expression level, as well as inhibition of ROS, increase of ADR accumulation in MCF7/ADR cells, and enhancement of ADR in inducing apoptosis of MCF7/ADR cells. As 14 has little toxic and side effects, it may have the potential for further research.

Discrimination of active and inactive substances in cytotoxicity based on Tox21 10K compound library: Structure alert and mode of action

In vitro cytotoxicity assay is an ideal alternative method for the in vivo toxicity in the risk assessment of pollutants in environment. However, modes of action (MOAs) of cytotoxicity have not been investigated for a wide range of compounds. In this paper, binomial and recursive partitioning analysis were carried out between the cytotoxicity and molecular descriptors for 8981 compounds. The results showed that cytotoxicity is strongly related to the chemical hydrophobicity and excess molar refraction, indicating the bio-uptake and chemical-receptor interaction through π and n electron pair play important roles in the cytotoxicity. The decision tree derived from recursive partitioning analysis revealed that the studied compounds could be divided into 25 groups and their structural characteristics could be used as structure alert to identify active and inactive compounds in cytotoxicity. The descriptors used in the decision tree revealed that chemical ionization and bioavailability could affect the cytotoxicity for ionizable and highly hydrophobic compounds. Comparison of MOAs based on Verhaar's classification scheme showed that many inert or less inert compounds were inactive substance, and many reactive or specifically-acting compounds were active substances in the cytotoxicity. In vitro toxicity assay instead of in vivo toxicity assay can be used in the environmental hazard and risk assessment of organic pollutants. The descriptors used in the binomial equation and decision tree reveal that chemical hydrophobicity, ionization and solubility play very important roles for identification of active and inactive compounds. The results obtained in this paper are valuable for understanding the modes of action in cytotoxicity and in vivo-in vitro toxicity relationship.

A Comprehensive Review on Fused Heterocyclic as DNA Intercalators: Promising Anticancer Agents

Since the discovery of DNA intercalating agents (by Lerman, 1961), a growing number of organic, inorganic, and metallic compounds have been developed to treat life-threatening microbial infections and cancers. Fused-heterocycles are amongst the most important group of compounds that have the ability to interact with DNA. DNA intercalators possess a planar aromatic ring structure that inserts itself between the base pairs of nucleic acids. Once inserted, the aromatic structure makes van der Waals interactions and hydrogen-bonding interactions with the base pairs. The DNA intercalator may also contain an ionizable group that can form ionic interactions with the negatively charged phosphate backbone. After the intercalation, other cellular processes could take place, leading ultimately to cell death. The heterocyclic nucleus present in the DNA intercalators can be considered as a pharmacophore that plays an instrumental role in dictating the affinity and selectivity exhibited by these compounds. In this work, we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation and cleaving and exert their antitumor activity. A general overview of the most recent results in this area, paying particular attention to compounds that are currently under clinical trials, is provided. Advancement in spectroscopic techniques studying DNA interaction can be examined in-depth, yielding important information on structure-activity relationships. In this comprehensive review, we have focused on the introduction to fused heterocyclic agents with DNA interacting features, from medicinal point of view. The structure-activity relationships points, cytotoxicity data, and binding data and future perspectives of medicinal compounds have been discussed in detail.

A straightforward, environmentally beneficial synthesis of spiro[diindeno[1,2-b:2',1'-e]pyridine-11,3'-indoline]-2',10,12-triones mediated by a nano-ordered reusable catalyst

A library of new spiro[diindeno[1,2-b:2',1'-e]pyridine-11,3'-indoline]-2',10,12-trione derivatives has been prepared in an efficient, one-pot pseudo four-component method mediated by a reusable heterogeneous nano-ordered mesoporous SO3H functionalized-silica (MCM-41-SO3H) catalyst. Excellent yields, short reaction times, as well as convenient non-chromatographic purification of the products and environmental benefits such as green and metal-free conditions constitute the main advantages of the developed synthetic methodology. The obtained fused indole-indenone dyes would be of interest to pharmaceutical and medicinal chemistry. Furthermore, due to their sensitivity to pH changes, they could be used as novel pH indicators.

Azafluorene derivatives as inhibitors of SARS CoV-2 RdRp: Synthesis, physicochemical, quantum chemical, modeling and molecular docking analysis

The crystal structures of 2-(1H-indol-3-yl)-4-phenyl-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ia) and 2-(1H-indol-3-yl)-4-(4-methoxyphenyl)-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ib) were determined using single crystal X-ray diffraction. Both the compounds belong to the triclinic system with the P-1 space group. The azafluorene ring system in both the compounds is effectively planar. The intermolecular interactions present in the compounds are discussed using Hirshfeld surface analysis, QTAIM and NCI. Compound Ib formed a strong interaction (-24.174 kJ/mol) with the solvent molecule. Both the compounds were geometry optimized using DFT/B3LYP level of theory. The compound's drug-like behaviors were studied using HOMO-LUMO analysis. The homology modeling of SARS CoV-2 RdRp was done utilizing the PDB 6NUR_A as a template. The model showed above 99% similarity with its preceder SARS CoV. The molecular docking analysis of the synthesized compounds was carried out along with some suggested drugs for COVID-19 and some phytochemicals. The docking results were then analyzed. The binding free energy of the complexes were calculated using MM-PB(GB)SA and ADMET properties of Ia and Ib were also predicted. Some suggestions are given from this analysis.

Construction of Dispiro-Indenone Scaffolds via Domino Cycloaddition Reactions of α,β-Unsaturated Aldimines with 2-Arylidene-1,3-indenediones and 2,2'-(Arylmethylene)bis(1,3-indenediones)

The catalyst-free domino reaction of α,β-unsaturated N-alkyl or N-arylaldimines with two molecules of 2-arylidene-1,3-indanediones in dry acetonitrile resulted in polysubstituted spiro[indene-2,3'-indeno[2',1':5,6]pyrano[2,3-b]pyridines] in moderate to good yields and with high diastereoselectivity. The reaction mechanism included sequential aza/oxa-Diels-Alder reactions via both endo-transition states. On the other hand, the catalyst-free domino reaction of α,β-unsaturated N-arylaldimines with 2,2'-(arylmethylene)bis(1,3-indenediones) afforded the mixed diastereoisomeric dispiro[indene-2,1'-cyclohexane-3',2″-indene] derivatives in satisfactory yields. The reaction mechanism of this formal [3 + 3] cycloaddition was believed to proceed with sequential nucleophilic 1,4-/1,2-additions.

A simple approach to indeno-coumarins via visible-light-induced cyclization of aryl alkynoates with diethyl bromomalonate

Visible-light-induced triple-domino cyclization between aryl alkynoates and diethyl bromomalonate was developed for the synthesis of indeno-coumarins.

Polyethylene glycol (PEG-400) promoted as an efficient and recyclable reaction medium for the one-pot eco-friendly synthesis of functionalized isoxazole substituted spirooxindole derivatives

An efficient, inexpensive and environmentally friendly synthesis of novel isoxazole substituted spirooxindole-pyridopyrimidine/indenopyridine/chromenopyridine/naphthyridine/quinoline derivatives has been developed.

Molecular structure studies of novel bronchodilatory-active 4-azafluorenes

Two 5H-indeno[1,2-b]pyridines, 7a and 7b, were synthesized and characterized by X-ray crystallography. In the molecular packing, molecules of 7a are linked into chains by C–H···N hydrogen bond which, in turn, are connected by H···π, N···π, Cl···π and π···π interactions. In the crystal structure of 7b, molecules are connected by C–H···N and C–H···Cl interactions as well as a set of N···π and Cl···π interactions. The molecular structures were studied by theory using AM1, PM3 and DFT. The basic difference between the theoretical and experimental structures was found in the relative orientation of dichlorophenyl ring attached to the indenopyridine residue, which was revealed to be aligned in nearly opposite orientations. This observation is attributed to the bulky chlorine atom(s) of the phenyl ring that prevent free rotation around the sigma bond attaching this ring with the heterocyclic system. DFT was used to determine the molecular electrostatic potential revealing the nitrile nitrogen to be the most nucleophilic site. A low HOMO-LUMO energy gap indicates high reactivity of 7a and 7b. The synthesized azafluorenes show more potent bronchodilation properties than the standard reference compound (theophylline).

BF3·Et2O mediated one-step synthesis of N-substituted-1,2-dihydropyridines, indenopyridines and 5,6-dihydroisoquinolines

A simple and efficient one-pot ring annulation provides quick access to N-substituted-1,2-dihydropyridines, indenopyridines and 5,6-dihydroisoquinolines.

Access to indenofurans and indenopyridines via annulation of heterocyclic ketene aminals, o-phthalaldehyde and cyclic 1,3-diketones

Access of indenofurans and indenopyridines through a one pot, three-component protocol.

Design, synthesis and anticancer activity of oxoaporphine alkaloid derivatives

A series of new oxoaporphine derivatives were synthesized and their inhibitory activity of topoisomerase I, cytotoxicity and DNA-binding properties were studied. Oxoaporphine can strongly inhibit topoisomerase I at concentrations of 5-50 µM and the cytotoxicity of the derivatives are more potent than their lead compound. Hypochromism, broadening and red shift in the absorption spectra were observed when these compounds bind to calf thymus DNA (CT DNA). These spectral characteristics were consistent with the intercalative binding of these compounds.

Synthesis and antiproliferative activity evaluation of imidazole-based indeno[1,2-b]quinoline-9,11-dione derivatives

A series of new imidazole substituted indeno[1,2-b]quinoline-9,11-dione derivatives were synthesized and evaluated for their antiproliferative effects on HeLa, LS180, MCF-7 and Jurkat human cancer cell lines. Antiproliferative effects were evaluated using MTT assay. Prepared compounds exhibited weak to good antiproliferative activity in evaluated cell lines. Prepared compounds were more potent in Jurkat cell line when compared to LS180, HeLa and MCF-7 cell lines. Compounds 29 (IC16 = 0.7 μM) and 31 (IC16 = 1.7 μM) and 33 (IC16 = 1.7 μM) were found to be the most potent molecules on Jurkat cell lines. Moreover; it was found that some of the tested compounds bearing imidazole-2-yl moiety on the C11-position of dihydropyridine ring exhibited superior antiproliferative activity in comparison to cis-platin especially in Jurkat cell line (compounds 29, 31, and 33). It seemed that the introduction of electron-withdrawing groups on the imidazole ring enhanced the antiproliferative potential of these compounds (compounds 27, 29 and 31). The results of this study proposed that some of the imidazole substituted indeno[1,2-b]quinoline-9,11-dione compounds may act as efficient anticancer agents in vitro, emphasizing their potential role as a source for rational design of potent antiproliferative agents.

One-pot, three-component synthesis of 7-azaindole derivatives from N-substituted 2-amino-4-cyanopyrroles, various aldehydes, and active methylene compounds

An efficient and practical route to 7-azaindole framework has been developed by one-pot, three-component cyclocondensation of N-substituted 2-amino-4-cyanopyrroles, various aldehydes, and active methylene compounds in ethanol or acetic acid at reflux. Reactions involving tetronic acid, indane-1,3-dione, dimedone, and 5-phenylcyclohexane-1,3-dione gave carbocyclic fused 7-azaindoles, whereas Meldrum's acid, benzoylacetonitrile, and malononitrile resulted in the highly substituted 7-azaindole derivatives, making this strategy very useful in diversity-oriented synthesis (DOS).