Structure–activity relationship (SAR) studies of quinoxalines as novel HCV NS5B RNA-dependent RNA polymerase inhibitors

Natural Products-Pyrazine Hybrids: A Review of Developments in Medicinal Chemistry

Pyrazine is a six-membered heterocyclic ring containing nitrogen, and many of its derivatives are biologically active compounds. References have been downloaded through Web of Science, PubMed, Science Direct, and SciFinder Scholar. The structure, biological activity, and mechanism of natural product derivatives containing pyrazine fragments reported from 2000 to September 2023 were reviewed. Publications reporting only the chemistry of pyrazine derivatives are beyond the scope of this review and have not been included. The results of research work show that pyrazine-modified natural product derivatives have a wide range of biological activities, including anti-inflammatory, anticancer, antibacterial, antiparasitic, and antioxidant activities. Many of these derivatives exhibit stronger pharmacodynamic activity and less toxicity than their parent compounds. This review has a certain reference value for the development of heterocyclic compounds, especially pyrazine natural product derivatives.

Reusable nano-catalyzed green protocols for the synthesis of quinoxalines: an overview

Heterocyclic compounds are very widely distributed in nature and are essential for life activities. They play a vital role in the metabolism of all living cells, for example, vitamins and co-enzyme precursors thiamine, riboflavin etc. Quinoxalines are a class of N-heterocycles that are present in a variety of natural and synthetic compounds. The distinct pharmacological activities of quinoxalines have attracted medicinal chemists considerably over the past few decades. Quinoxaline-based compounds possess extensive potential applications as medicinal drugs, presently; more than fifteen drugs are available for the treatment of different diseases. Diverse synthetic protocols have been developed via a one-pot approach using efficient catalysts, reagents, and nano-composites/nanocatalysts etc. But the use of homogeneous and transition metal-based catalysts suffers some demerits such as low atom economy, recovery of catalysts, harsh reaction conditions, extended reaction period, expensive catalysts, the formation of by-products, and unsatisfactory yield of products as well as toxic solvents. These drawbacks have shifted the attention of chemists/researchers to develop green and efficient protocols for synthesizing quinoxaline derivatives. In this context, many efficient methods have been developed for the synthesis of quinoxalines using nanocatalysts or nanostructures. In this review, we have summarized the recent progress (till 2023) in the nano-catalyzed synthesis of quinoxalines using condensation of o-phenylenediamine with diketone/other reagents with plausible mechanistic details. With this review, we hope that some more efficient ways of synthesizing quinoxalines can be developed by synthetic chemists.

Orally Bioavailable Quinoxaline Inhibitors of 15-Prostaglandin Dehydrogenase (15-PGDH) Promote Tissue Repair and Regeneration

15-Prostaglandin dehydrogenase (15-PGDH) regulates the concentration of prostaglandin E2 in vivo. Inhibitors of 15-PGDH elevate PGE2 levels and promote tissue repair and regeneration. Here, we describe a novel class of quinoxaline amides that show potent inhibition of 15-PGDH, good oral bioavailability, and protective activity in mouse models of ulcerative colitis and recovery from bone marrow transplantation.

Accessing oxy-functionalized N-heterocycles through rose bengal and TBHP integrated photoredox C(sp3)–O cross-coupling

A C(sp3)–O coupling strategy is described involving tautomerizable N-heterocycles (phthalazinone, pyridne, pyrimidinone and quinoxalinone) carbonyl employing rose bengal as the photocatalyst and TBHP.

Natural vs. Synthetic Phosphate as Efficient Heterogeneous Compounds for Synthesis of Quinoxalines

Natural phosphate (NP) and synthetic fluorapatite phosphate (SFAP) were proposed as stable, inexpensive, readily available and recyclable catalysts for the condensation of 1,2-diamines with 1,2-dicarbonyls in methanol to afford quinoxaline at room temperature. NP provided as high as 92-99% yield for quinoxalines in short reaction times (i.e., 1-45 min), while SFAP created quinoxalines with 87-97% yield in 60-120 min. From the chemical analyses, X-ray fluoresecency, X-ray diffraction, energy dispersive X-ray and Fourier-transform infrared spectroscopy methods, two main phases (CaO, P2O5) appeared in NP together with other low content phases (SiO2, Fe2O3). Compared to other phases, apatite (CaO and P2O5 as Ca10(PO4)6) played a major role in the catalytic activity of NP. SFAP with similar Ca/P atomic ratio showed a relatively lower catalytic activity than NP for the condensation of 1,2-diamine with 1,2-dicarbonyl in methanol at ambient temperature. To investigate the recyclability of catalysts, the surface properties of NP and 6-recycled NP were investigated using scanning electron microscopy, energy dispersive X-ray and Brunauer-Emmett-Teller and Barrett-Joyner-Halenda methods. Some differences were observed in NP and 6-recycled NP's particle size, surface area, the volume and size of pores, and the content of elements; nevertheless, the use-reuse process did not noticeably change the catalytic property of NP.

Regioselective Synthesis of Trisubstituted Quinoxalines Mediated by Hypervalent Iodine Reagents

A facile and regioselective synthesis of quinoxalines, an important motif in medicinal chemistry and materials sciences, was developed. Despite their prospective utility, the regioselective preparation of trisubstituted quinoxalines has not been previously established. In the reported system, hypervalent iodine reagents catalyzed the annulation between α-iminoethanones and o-phenylenediamines in a chemo/regioselective manner to afford trisubstituted quinoxalines. Excellent regioselectivities (6:1 to 1:0) were achieved using [bis(trifluoroacetoxy)iodo]benzene and [bis(trifluoroacetoxy)iodo]pentafluorobenzene as annulation catalysts.

Mitochondria-Targeting Click-Derived Pyridinyltriazolylmethylquinoxaline-Based Y-Shaped Binuclear Luminescent Ruthenium(II) and Iridium(III) Complexes as Cancer Theranostic Agents

Due to several negative issues, market available drugs have been gradually losing their importance in the treatment of cancer. With a view to discover suitable drugs capable of diagnosing as well as inhibiting the growth of cancer cells, we have aspired to develop a group of theranostic metal complexes which will be (i) target specific, (ii) cytoselective, thus rendering the normal cell unaffected, (iii) water-soluble, (iv) cancer cell permeable, and (v) luminescent, being beneficial for healing the cancer eternally. Therefore, to reach our goal, we have prepared novel Ru(II)- and Ir(III)-based bimetallic and hetero bimetallic scaffolds using click-derived pyridinyltriazolylmethylquinoxaline ligands followed by metal coordination. Most of the compounds have displayed significant cytoselectivity against colorectal adenocarcinoma (Caco-2) and epithiloid cervical carcinoma (HeLa) cells with respect to normal human embryonic kidney cells (HEK-293) compared to cisplatin [cis-diamminedichloroplatinum(II)] along with excellent binding efficacy with DNA as well as serum albumin. Complex [(η⁶-p-cymene)(η⁵-Cp*)Ru^IIIr^IIICl₂(K²-N,N-L)](PF₆)₂ [RuIrL] exhibited the best cytoselectivity against all the human cancer cells and was identified as the most significant cancer theranostic agent in terms of potency, selectivity, and fluorescence quantum yield. Investigation of the localization of complex [Ir₂L] and [RuIrL] in the more aggressive colorectal adenocarcinoma cell HT-29 indicates that mitochondria are the key cellular target for destroying cancer cells. Mitochondrial dysfunction and G2/M phase cell cycle arrest in HT-29 cell were found to be involved in the apoptotic cell death pathway induced by the test complexes [Ir₂L] and [RuIrL]. These results validate the concept that these types of complexes will be reasonably able to exert great potential for tumor diagnosis as well as therapy in the near future.

Cu(ii), Ir(i) and CuO nanocatalyzed mild synthesis of luminescent symmetrical and unsymmetrical bis(triazolylmethyl)quinoxalines: biocompatibility, cytotoxicity, live cell imaging and biomolecular interaction

A microwave induced Cu(ii) and Ir(i) catalysed click reaction for the synthesis of anticancer symmetrical and unsymmetrical triazoles.

Catalyst-free direct cross-dehydrogenative coupling of imidazoheterocycles with glyoxal hydrates: an efficient approach to 1,2-diketones

An efficient and convenient methodology for catalyst-free cross-dehydrogenative coupling of imidazoheterocycles with glyoxal hydrates in good yields was developed. This methodology exhibits a broad substrate scope and excellent functional group tolerance and offers a straightforward means to produce different heterocycles such as imidazoheterocyclic quinoxaline, imidazoheterocyclic hydantoin and imidazoheterocyclic α-keto ketamine under relatively mild conditions. Biological evaluation showed that the most potent compound 3m possesses significant in vitro antiproliferative activities against human-derived lung cancer cell lines with an IC50 value of 14.8 μM.

Construction of a novel quinoxaline as a new class of Nrf2 activator

Background

The transcription factor Nuclear factor erythroid-2-related factor 2 (NRF2) and its principal repressive regulator, Kelch-like ECH-associated protein 1 (KEAP1), are perilous in the regulation of inflammation, as well as maintenance of homeostasis. Thus, NRF2 activation is involved in cytoprotection against many inflammatory disorders. N′-Nicotinoylquinoxaline-2-carbohdyrazide (NQC) was structurally designed by the combination of important pharmacophoric features of bioactive compounds reported in the literature.

Methods

NQC was synthesised and characterised using spectroscopic techniques. The compound was tested for its anti-inflammatory effect using Lipopolysaccharide from Escherichia coli (LPSEc) induced inflammation in mouse macrophages (RAW 264.7 cells). The effect of NQC on inflammatory cytokines was measured using enzyme-linked immune sorbent assay (ELISA). The Nrf2 activity of the compound NQC was determined using ‘Keap1:Nrf2 Inhibitor Screening Assay Kit’. To obtain the insights on NQC’s activity on Nrf2, molecular docking studies were performed using Schrödinger suite. The metabolic stability of NQC was determined using mouse, rat and human microsomes.

Results

NQC was found to be non-toxic at the dose of 50 µM on RAW 264.7 cells. NQC showed potent anti-inflammatory effect in an in vitro model of LPSEc stimulated murine macrophages (RAW 264.7 cells) with an IC₅₀ value 26.13 ± 1.17 µM. NQC dose-dependently down-regulated the pro-inflammatory cytokines [interleukin (IL)-1β (13.27 ± 2.37 μM), IL-6 (10.13 ± 0.58 μM) and tumor necrosis factor (TNF)-α] (14.41 ± 1.83 μM); and inflammatory mediator, prostaglandin E₂ (PGE₂) with IC₅₀ values, 15.23 ± 0.91 µM. Molecular docking studies confirmed the favourable binding of NQC at Kelch domain of Keap-1. It disrupts the Nrf2 interaction with kelch domain of keap 1 and its IC₅₀ value was 4.21 ± 0.89 µM. The metabolic stability studies of NQC in human, rat and mouse liver microsomes revealed that it is quite stable with half-life values; 63.30 ± 1.73, 52.23 ± 0.81, 24.55 ± 1.13 min; microsomal intrinsic clearance values; 1.14 ± 0.31, 1.39 ± 0.87 and 2.96 ± 0.34 µL/min/g liver; respectively. It is observed that rat has comparable metabolic profile with human, thus, rat could be used as an in vivo model for prediction of pharmacokinetics and metabolism profiles of NQC in human.

Conclusion

NQC is a new class of NRF2 activator with potent in vitro anti-inflammatory activity and good metabolic stability.

Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions

Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.

Discovery of hit molecules targeting allosteric site of hepatitis C virus NS5B polymerase

Nonstructural protein 5B (NS5B), the RNA-dependent RNA polymerase of Hepatitis C Virus (HCV), plays a key role in viral amplification and is an attractive and most explored target for discovery of new therapeutic agents for Hepatitis C. Though safe and effective, NS5B inhibitors were launched in 2013 (Sovaldi) and 2014 (Harvoni, Viekira Pak), the high price tags of these medications limit their use among poor people in developing countries. Hence, still there exists a need for cost-effective and short duration anti-HCV agents especially those targeting niche patient population who were non-respondent to earlier therapies or with comorbid conditions. The present study describes the discovery of novel non-nucleoside (NNI) inhibitors of NS5B using a series of rational drug design techniques such as virtual screening, scaffold matching and molecular docking. 2D and 3D structure based virtual screening technique identified 300 hit compounds. Top 20 hits were screened out from identified hits using molecular docking technique. Four molecules, that are representative of 20 hits were evaluated for binding affinity under in vitro conditions using surface plasmon resonance-based assay and the results emphasized that compound with CoCoCo ID: 412075 could exhibit good binding response toward NS5B and could be a potential candidate as NS5B inhibitor.Communicated by Ramaswamy H. Sarma.

Comparative Molecular Field Analysis and Molecular Docking Studies on Quinolinone Derivatives Indicate Potential Hepatitis C Virus Inhibitors

Presently, there are no effective vaccines and anti-virals for the prevention and treatment of Hepatitis C virus infections and hence there is an urgent need to develop potent HCV inhibitors. In this study, we have carried out molecular docking, molecular dynamics and 3D-QSAR on heteroaryl 3-(1,1-dioxo-2H-(1,2,4)-benzothiadizin-3-yl)-4-hydroxy-2(1H)-quinolinone series using NS5B protein. Total of 41 quinolinone derivatives is used for molecular modeling study. The binding conformation and hydrogen bond interaction of the docked complexes were analyzed to model the inhibitors. We identified the molecule XXXV that had a higher affinity with NS5B. The molecular dynamics study confirmed the stability of the compound XXXV-NS5B complex. The developed CoMFA descriptors parameters, which were calculated using a test set of 13 compounds, were statistically significant. Our results will provide useful insights and lead to design potent anti-Hepatitis C virus molecules.

Recent Advances in Homogeneous Metal-Catalyzed Aerobic C–H Oxidation of Benzylic Compounds

Csp3–H oxidation of benzylic methylene compounds is an established strategy for the synthesis of aromatic ketones, esters, and amides. The need for more sustainable oxidizers has encouraged researchers to explore the use of molecular oxygen. In particular, homogeneous metal-catalyzed aerobic oxidation of benzylic methylenes has attracted much attention. This account summarizes the development of this oxidative strategy in the last two decades, examining key factors such as reaction yields, substrate:catalyst ratio, substrate scope, selectivity over other oxidation byproducts, and reaction conditions including solvents and temperature. Finally, several mechanistic proposals to explain the observed results will be discussed.

Synthesis of α-keto imides through copper-catalyzed oxidation of N-sulfonyl ynamides

A novel copper-catalyzed N-oxide oxidation of N-sulfonyl ynamides is disclosed. This non-noble metal-catalyzed protocol enables facile and efficient access to valuable α-keto imides in generally good to excellent yields. Other notable features of this method include widespread availability of the substrates, compatibility with broad functional groups, a simple procedure, mild conditions, and in particular, no need to exclude moisture or air ("open flask").

Design, synthesis, molecular docking of new lipophilic acetamide derivatives affording potential anticancer and antimicrobial agents

Fifteen new substituted N-2-(2-oxo-3-phenylquinoxalin-1(2H)-yl) acetamides 5a-f, 6a-f, and 8a-c were synthesized by reacting ethyl 2-(2-oxo-3-phenylquinoxalin-1(2H)-yl)acetate with various primary amines including benzylamines, sulfonamides, and amino acids. The in vitro antimicrobial screening of the target compounds was screened to assess their antibacterial and antifungal activity. As a result, seven compounds namely; 5a, 5c, 5d, 6a, 6c, 8b and 8c showed a promising broad spectrum antibacterial activity against both Gram-positive and Gram-negative strains. Among these, the analogs 5c and 6d were nearly as equiactive as ciprofloxacin drug. Meanwhile, four compounds namely; 5c, 6a, 6f and 8c exhibited appreciable antifungal activity with MIC values range 33-40 mg/mL comparable with clotrimazole (MIC 25 mg/mL). In addition, the anticancer effects of the synthesized compounds were evaluated against three cancer lines. The data obtained revealed the benzylamines and sulpha derivatives were the most active compounds especially 5f and 6f ones. Further EGFR enzymatic investigation was carried out for these most active compounds 5f and 6f resulting in inhibitory activity by 1.89 and 2.05 µM respectively. Docking simulation was performed as a trial to study the mechanisms and binding modes of these compounds toward the enzyme target, EGFR protein kinase enzyme. The results revealed good compounds placement in the active sites and stable interactions similar to the co-crystallized reference ligand. Collectively, the analogs 5f and 6f could be further utilized and optimized as good cytotoxic agents.

Deciphering molecular properties and docking studies of hepatitis C and non-hepatitis C antiviral inhibitors - A computational approach

BACKGROUND

Hepatitis C is an infectious liver disease with high mortality rate which is caused by Hepatitis C virus. Several treatment methods have been applied to combat this deadly virus including interferons, vaccine and direct acting antivirals (DAAs). However, the later shows promising effects in HCV treatment with lower adverse effect. Specifically, the DAAs target the non-structural proteins (NS3 and NS5B).

PURPOSE

The objective of the present study is to hypothesize an alternative antiviral inhibitor for HCV from the available other antivirals.

METHODS

Computation of 2D molecular descriptors for the selected antiviral inhibitors followed by clustering the descriptor features. The closely clustered compounds were subjected to the interaction studies against the HCV target protein to validate the cluster result.

RESULTS AND DISCUSSION

The clustering result showed that indinavir (HIV inhibitor) and AT130 (HBV inhibitor) molecule are close to the HCV inhibitor. The indinavir complexed with NS3 protein shows -5.33kcal/mol and AT-130 complexed with NS5B protein possess the binding energy of -8.87kcal/mol. The docking interaction study indicated a better binding affinity than other viral inhibitors.

CONCLUSION

From the descriptor based feature similarity analysis and the interaction study, it can be concluded that indinavir and AT-130 could be a potential alternative agent for HCV treatment.

An Efficient and Recyclable Nanoparticle-Supported Cobalt Catalyst for Quinoxaline Synthesis

The syntheses of quinoxalines derived from 1,2-diamine and 1,2-dicarbonyl compounds under mild reaction conditions was carried out using a nanoparticle-supported cobalt catalyst. The supported nanocatalyst exhibited excellent activity and stability and it could be reused for at least ten times without any loss of activity. No cobalt contamination could be detected in the products by AAS measurements, pointing to the excellent activity and stability of the Co nanomaterial.