Structure-activity relationships for analogues of the phenazine-based dual topoisomerase I/II inhibitor XR11576

Practice of green chemistry strategies in synthetic organic chemistry: a glimpse of our sincere efforts in green chemistry research

This feature article summarises our recent contributions (2019-2023) in designing and developing a handful of promising organic transformations for accessing several diversely functionalised biologically relevant organic scaffolds, following the green chemistry principles, particularly focusing on the application of low-energy visible light, electrochemistry, ball-milling, ultrasound, and catalyst- and additive-free synthetic strategies.

A review on lawsone-based benzo[a]phenazin-5-ol: synthetic approaches and reactions

Phenazine systems are an important class of aza-polycyclic compounds that are easily found in nature and isolated as secondary metabolites primarily from Pseudomonas, Streptomyces, and a few other genera from soil or marine habitats. Moreover, various synthetic phenazine analogs are known for their pharmaceutical activities. Among various phenazines, benzo[a]phenazines are structural subunits in a variety of important natural products and have been given special attention due to their unique biological properties in various fields. In this review article, we highlight the synthesis of benzo[a]phenazin-5-ol derivatives from lawsone and benzene-1,2-diamines and their applications for the construction of a variety of five and six membered fused heterocycles such as pyranophenazines, spiropyranophenazines, pyridophenazines, furophenazines, benzochromenophenazines and oxazinophenazines during the period of 1995 to 2021.

Photochemical and electrochemical regioselective cross-dehydrogenative C(sp2)–H sulfenylation and selenylation of substituted benzo[a]phenazin-5-ols

The essence of photo- and electrochemistry: sulfenylation and selenylation of substituted benzo[a]phenazin-5-ols through cross-dehydrogenative C(sp2)–H functionalization.

Novel DNA Bis-Intercalator XR5944 as a Potent Anticancer Drug-Design and Mechanism of Action

This review is dedicated to Professor William A. Denny’s discovery of XR5944 (also known as MLN944). XR5944 is a DNA-targeted agent with exceptionally potent antitumor activity and a novel DNA binding mode, bis-intercalation and major groove binding, as well as a novel mechanism of action, transcription inhibition. This novel anticancer compound represents a remarkable accomplishment resulting from two decades of drug discovery by Professor Denny and coworkers. Here, we review our work on the structural study of the DNA binding mode of XR5944 and mechanistic study of XR5944 action.

Synthesis and biological evaluation of novel benzo[a]pyridazino[3,4-c]phenazine derivatives

A convenient microwave-assisted one-pot four-component synthetic approach was developed en route to novel functionalized benzo[a]pyridazino[3,4-c]phenazine derivatives starting from 2-hydroxy-1,4-naphthoquinone, aromatic aldehydes, methyl hydrazine and o-phenylenediamine. Nine new derivatives were successfully synthesized and subsequently evaluated in terms of their biological profiles. The results revealed good cytotoxic activities of compounds 6a, 6h against KB, HepG2, Lu1 and MCF7 human cancer cell lines. Besides that, compound 6d exhibited promising antimicrobial activities toward Staphylococcuc aureus and Bacillus subtilis bacterial strains with IC₅₀ < 6 μM.

Synthesis and Biological Activity of Ferrocenyl and Ruthenocenyl Analogues of Etoposide: Discovery of a Novel Dual Inhibitor of Topoisomerase II Activity and Tubulin Polymerization

Two series of the ferrocenyl and ruthenocenyl analogues of etoposide bearing 1,2,3-triazolyl or aminoalkyl linker were synthesized and evaluated for their cytotoxic properties, influence on the cell cycle, ability to induce tubulin polymerization, and inhibition of topoisomerase II activity. We found that the replacement of the etoposide carbohydrate moiety with a metallocenyl group led to organometallic conjugates exhibiting differentiated antiproliferative activity. Biological studies demonstrated that two ferrocenylalkylamino conjugates were notably more active than etoposide, with submicromolar or low-micromolar IC₅₀ values towards SW620, etoposide-resistant SW620E, and methotrexate-resistant SW620M cancer cell lines. Moreover, the simplest ferrocenylmethylamino conjugate exerted dual inhibitory action against tubulin polymerization and topoisomerase II activity while other studied compounds affected only topoisomerase II activity.

Topoisomerase II as a target for repurposed antibiotics in Candida albicans: an in silico study

Fluoroquinolines, the widely used antibacterial antibiotics, have been shown to interact with human DNA topoisomerases supporting their use as repurposed cancer drugs in humans. In this communication molecular docking of eleven Fluoroquinolines against predicted structure of Candida albicans DNA Topoisomerase II is reported for the first time. C. albicans topoisomerase II structure prediction was done by using homology modeling tool. Ligand preparation and molecular docking with C. albicans topoisomerase II were done by using Autodock tool. These antibiotics formed hydrogen bond with good binding affinity at ARG 841, GLN803, ALA840 amino acid residues in the active site of C. albicans Topoisomerase II. We hypothesize that DNA toposiomerases may be the targets of Fluroquinoline group of antibiotics in C. albicans causing inhibition of growth.

A High-Throughput Screening Method for Determining the Optimized Synthesis Conditions of Quinoxaline Derivatives Using Microdroplet Reaction

Quinoxaline derivatives demonstrate many distinguished chemical, biological, and physical properties and have a wide application in dyes, electroluminescent material, organic semiconductors, biological agents, etc. However, the synthesis of quinoxaline still suffers from several drawbacks, for instance, longer reaction time, unsatisfactory yields, and use of metal catalysts. Here, utilizing microdroplet-assisted reaction, we demonstrate the successive synthesis of several important quinoxaline derivatives. For case studies of 1H-indeno [1, 2-b] quinoxaline and 3,5-dimethyl-2-phenylquinoxaline, the present microdroplet approach can complete in milliseconds and the conversion rate reached 90% without adding any catalyst, which is considerably quicker and higher than conversional bulk-phase reactions. When combined with MS detection, high-throughput screening of the optimal reaction conditions can be achieved. Several impacts of droplet volume, reaction flow rate, distance from the MS inlet, spray voltage, and flow rate of the auxiliary gas can be screened on-site quickly for enhanced reaction speed and yields. More importantly, this platform is capable to be used for the scaled-up microdroplet synthesis of quinoxaline diversities. Considering the facile, economic, and environmentally friendly features of the microdroplet approach, we sincerely hope that the current strategy can effectively promote the academic research and industrial fabrications of functional quinoxaline substances for chemical, biological, and pharmaceutical application developments.

Structural Recognition and Binding Pattern Analysis of Human Topoisomerase II Alpha with Steroidal Drugs: In Silico Study to Switchover the Cancer Treatment

BACKGROUND AND OBJECTIVE

Topoisomerase TOP-IIA (TTOP-IIA) is widely used as a significant target for cancer therapeutics because of its involvement in cell proliferation. Steroidal drugs have been suggested for breast cancer treatment as aromatase enzymes inhibitors . TTOP-IIA inhibitors can be used as a target for the development of new cancer therapeutics.

MATERIALS AND METHODS

In this study, we conducted a docking study on steroidal drugs Anastrozole (ANA), Letrozole (LET), and exemestane (EXE) with TTOP-IIA  to explore the therapeutic area of these drugs.

RESULTS

The binding interaction of EXE drug had significant docking interaction which is followed by ANA and LET. Thus, all these drugs could be used to inhibit the TTOP-IIA mediated cell proliferation and could be a hope to treat the other types of cancers. Among all three tested steroidal drugs, EXE showed binding energy -7.05 kcal/mol, hydrogen bond length1.78289 Å and amino acid involved in an interaction was A: LYS723:HZ3 -: UNK1:O6.

CONCLUSION

The obtained data showed the most significant binding interaction analyzed with the tested enzyme. Thus, in vitro laboratory experimentation and in vivo research are necessary to put forward therapeutic repositioning of these drugs to establish them as a broad spectrum potential anticancer drugs.
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An efficient and environmentally sustainable domino protocol for the synthesis of structurally diverse spiroannulated pyrimidophenazines using erbium doped TiO2 nanoparticles as a recyclable and reusable heterogeneous acid catalyst

An efficient and environmentally sustainable domino protocol has been presented for the synthesis of structurally diverse spiroannulated pyrimidophenazines involving a four component reaction of 2-hydroxynaphthalene-1,4-dione, benzene-1,2-diamine, cyclic ketones and amino derivatives in the presence of erbium doped TiO2 nanoparticles as a recyclable and reusable heterogeneous acid catalyst. The present synthetic protocol features mild reaction conditions with operational simplicity, excellent yield with high purity, short reaction time and high atom economy with the use of a recoverable and reusable environmentally sustainable heterogeneous catalyst.

Regioselective 6-endo-dig iodocyclization: an accessible approach for iodo-benzo[a]phenazines

A facile approach for the synthesis of substituted iodo-benzo[a]phenazines from 2-aryl-3-(aryl/alkylethynyl)quinoxalines via 6-endo-dig ring closure has been described under mild reaction conditions. Iodocyclization proceeds through the iodonium ion intermediate followed by nucleophilic cyclization with the C-H bond of the arene. Furthermore, the resulting 6-iodo-5-aryl/alkyl benzo[a]phenazine derivatives allowed for structural diversification by employing various coupling reactions. The structure of iodo-benzo[a]phenazine was confirmed by X-ray crystallographic studies of the compound.

Molecular docking studies on thirteen fluoroquinolines with human topoisomerase II a and b

DNA relaxation is an important step in DNA replication. DNA topoisomerases play a major role in DNA relaxation. Hence these enzymes are important targets for cancer drugs. DNA topoisomerase inhibitors bind to the transient enzyme-DNA complex and inhibit DNA replication. Various inhibitors of topoisomerase I and II are prescribed as drugs. Topoisomerase II is considered as an important target for the development of anticancer drugs. In this study we have demonstrated molecular docking of thirteen fluoroquinolines with human DNA topoisomerase II alpha (a) and beta (b). Fluoroquinolines are broad spectrum antibacterial antibiotics and it is highly effective against various bacterial infections. Some of the fluoroquinolines like moxifloxacin exert antifungal as well as anti-cancer activity. It forms complexes with topoisomerase II a and are responsible for stoppage DNA replication. Molecular docking studies showed that fluoroquinolines has shown formation of hydrogen bond and good binding affinity with human Topo2a and Topo2b. Hence FQs may inhibit the activity of enzyme topoisomerase by binding at its active site. Ofloxacin, sparafloxacin, ciprofloxacin and moxifloxacin are predicted to be the most potent inhibitors among the thirteen FQs docked. GLN773, ASN770, LYS723 and TRP931 amino acid residues of Topo2a are involved in binding with FQs while ASP479, SER480, ARG820, ARG503, LYS456 and GLN778 amino acid residues of Topo2b are involved in binding with FQs. Our in silico study suggests that fluoroquinolines could be repositioned as DNA topoisomerase II inhibitors hence can be used as anticancer drugs. In vitro and in vivo experiments need to be done to confirm their efficacy.

Prediction of noncovalent Drug/DNA interaction using computational docking models: studies with over 1350 launched drugs

Noncovalent chemical/DNA interactions, for example, intercalation and groove-binding, may be more important to genomic integrity than previously appreciated, and there may very well be genotoxic consequences of that binding. It is of importance, then, to develop methods allowing a determination or prediction of such interactions. This would have particular utility in the pharmaceutical industry where genotoxicity is, for the most part, disallowed in new drug entities. We have previously used DNA docking simulations to assess if molecules had structure and charge characteristics which could accommodate noncovalent binding via, for example, electrostatic/hydrogen bonding. We here extend those earlier studies by examining a series of over 1,350 "launched" drugs for ability to noncovalently bind 10 different DNA sequences using two computational programs: Autodock and Surflex. These drugs were also evaluated for binding to the crystallographic ATP-binding site of human topoisomerase II. The results obtained clearly demonstrate multiple series of noncovalent DNA binding structure activity relationships which would not have been predicted based on cursory structural examination. Many drugs within these series are genotoxic although not via any commonly recognized structural covalent alerts. The present studies confirm previously implicated features such as N-dialkyl groups and specific N-aryl ketones as potential genotoxic chemical moieties acting through noncovalent mechanisms. These initial studies provide considerable evidence that DNA intercalation may be an important, largely overlooked, source of drug-induced genotoxicity and further suggest involvement of topoisomerase in that genotoxicity.

Multicomponent synthesis of poly-substituted benzo[a]pyrano[2,3-c]phenazine derivatives under microwave heating

A new one-pot two-step tandem synthesis of highly functionalized benzo[a]pyrano[2,3-c]phenazine derivatives via microwave-assisted multicomponent reactions of 2-hydroxynaphthalene-1,4-dione, diamines, aldehydes, and malononitrile is reported. The procedures are facile, avoiding time-consuming and costly syntheses, tedious workup, and purifications of precursors, as well as protection/deprotection of functional groups. The method is expected to find application in the combinatorial synthesis of biologically active compounds, since phenazine and chromene motifs have a broad spectrum of biological activities.

Configurational assignment of carbon, silicon and germanium containing propynal oximes by means of 13C-1H, 13C-13C and 15N-1H spin-spin coupling constants

Configurational assignment of five carbon, silicon and germanium containing propynal oximes has been carried out by means of experimental measurements and high-level ab initio calculations of their 13C-1H, 13C-13C and 15N-1H spin-spin coupling constants. The title compounds were shown to exist in the nonequilibrium mixture of E and Z isomers with the energy difference of less than 0.3 kcal/mol calculated at the MP2/6-311G** level.

QSAR studies about cytotoxicity of benzophenazines with dual inhibition toward both topoisomerases I and II: 3D-MoRSE descriptors and statistical considerations about variable selection

Deoxyribonucleic acid (DNA) topoisomerases are involved in diverse cellular processes, such as replication, transcription, recombination, and chromosome segregation. Searching new compounds that inhibit both topoisomerases I and II is very important due to the deficiency of the specific inhibitors to overcome multidrug resistance (MDR). A QSAR study was developed, employing the 3D-MoRSE descriptors and a set of 64 benzophenazines in order to model the inhibition of the topoisomerases I and II, expressed by the cytotoxicity of these compounds (IC(50)) versus drug-resistant human small cell lung carcinoma line cell H69/LX4. A comparison with other approaches such as the Topological, BCUT, Galvez topological charge indexes, 2D autocorrelations, Randić molecular profile, Geometrical, RDF, and WHIM descriptors was carried out. The mathematical models were obtained by means of the multiple regression analysis (MRA) and the variables were selected using the genetic algorithm. The model relative to the 3D-MoRSE descriptors was considered as the best, taking into account its statistical parameters. It was able to describe more than 82.2% of the variance in the experimental activity once the outliers were extracted.

Novel synthetic isoquinolino[5,4-ab]phenazines: Inhibition toward topoisomerase I, antitumor and DNA photo-cleaving activities

The novel DNA interactive isoquinolino[5,4-ab]phenazine derivatives were designed and synthesized. Their inhibitory abilities toward topoisomerase I, antitumor activities and DNA photo-cleaving abilities were examined. The substituents at peri sites of two phenazine N atoms played very important roles for all these biological activities. At a concentration of 100 microM, all these phenazine derivatives (but A2 and A6) exhibited an inhibitory activity toward topoisomerase I. A6 had efficient antitumor activities against both human lung cancer cell (A549) and murine leukemia cell (P388). A1, A5, and A6 exhibited antitumor activities selectively against P388. A2 was the most efficient DNA photocleaver, which had converted supercoiled DNA from form I to form II at <1 microM. Under anaerobic conditions, the electron transfer mechanism mainly contributed to DNA photo-induced cleavage, while under aerobic conditions, superoxide anion was also involved in this process.

Phase I and pharmacokinetic study of XR11576, an oral topoisomerase I and II inhibitor, administered on days 1-5 of a 3-weekly cycle in patients with advanced solid tumours

XR11576 is an oral topoisomerase I and II inhibitor. The objectives of this phase I study were to assess the dose-limiting toxicities (DLTs), to determine the maximum tolerated dose (MTD) and to describe the pharmacokinetics (PKs) of XR11576 when administered orally on days 1–5 every 3 weeks to patients with advanced solid tumours. Patients were treated with escalating doses of XR11576 at doses ranging from 30 to 180 mg day⁻¹. For PK analysis, plasma sampling was performed during the first and second courses of treatment and XR11576 concentrations were assayed using a validated high-performance liquid chromatographic assay with mass spectrometric detection. In all, 21 patients received a total of 47 courses. The MTD was reached at 180 mg day⁻¹, with diarrhoea and fatigue as DLT. Nausea and vomiting, although not qualifying for DLT, was ubiquitous. Only in combination with an extensive prophylactic antiemetic regimen consisting of a combination of both dexamethasone and a 5HT3 antagonist was treatment with XR11576 at 120 mg day⁻¹ tolerable. The systemic exposure of XR11576 increased more than proportionally with increasing dose, with a large interpatient variability. No objective responses were seen; four patients experienced stable disease for periods of 12–30 weeks. In this study, the DLTs of XR11576 were diarrhoea and fatigue. The recommended dose for phase II studies of XR11576 is 120 mg administered orally, on days 1–5 every 21 days. Alternative regimens are currently being explored.