In search of uracil derivatives as bioactive agents. Uracils and fused uracils: Synthesis, biological activity and applications

Synthesis and Evaluation of Some Uracil Nucleosides as Promising Anti-Herpes Simplex Virus 1 Agents

Since herpes simplex virus type 1 (HSV-1) infection is so widespread, several antiviral drugs have been developed to treat it, among which are uracil nucleosides. However, there are major problems with the current medications such as severe side-effects and drug resistance. Here we present some newly synthesized cyclic and acyclic uracil nucleosides that showed very promising activity against HSV-1 compared to acyclovir.

Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications

The gas-phase acidity and proton affinity (PA) of 5-halouracils (5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil) have been examined using both theoretical and experimental methods. This work represents a comprehensive study of the thermochemical properties of these nucleobases. Other than 5-fluorouracil acidity, the intrinsic acidity and PA of these halouracils have not been heretofore measured; these new experimental data provide a benchmark for the computational values. Furthermore, we examine these 5-halouracils in the context of the enzyme thymine DNA glycosylase (TDG), which is an enzyme that protects the genome by cleaving these substrates from DNA. Our gas-phase results are compared and contrasted to TDG excision rates to afford insights into the TDG mechanism.

Synthesis and Rational Design of New Appended 1,2,3-Triazole-uracil Ensembles as Promising Anti-Tumor Agents via In Silico VEGFR-2 Transferase Inhibition

Angiogenesis inhibition is a key step towards the designing of new chemotherapeutic agents. In a view to preparing new molecular entities for cancer treatment, eighteen 1,2,3-triazole-uracil ensembles 5a-r were designed and synthesized via the click reaction. The ligands were well characterized using 1H-, 13C-NMR, elemental analysis and ESI-mass spectrometry. The in silico binding propinquities of the ligands were studied sequentially in the active region of VEGFR-2 using the Molegro virtual docker. All the compounds produced remarkable interactions and potentially inhibitory ligands against VEGFR-2 were obtained with high negative binding energies. Drug-likeness was assessed from the ADME properties. Cytotoxicity of the test compounds was measured against HeLa and HUH-7 tumor cells and NIH/3T3 normal cells by MTT assay. Compound 5h showed higher growth inhibition activity than the positive control, 5-fluorouracil (5-FU), against both HeLa and HUH-7 cells with IC50 values of 4.5 and 7.7 μM respectively. Interestingly, the compounds 5a-r did not show any cytotoxicity towards the normal cell lines. The results advance the position of substituted triazoles in the area of drug design with no ambiguity.

Use of a molecular beacon based fluorescent method for assaying uracil DNA glycosylase (Ung) activity and inhibitor screening

Uracil DNA glycosylases are an important class of enzymes that hydrolyze the N-glycosidic bond between the uracil base and the deoxyribose sugar to initiate uracil excision repair. Uracil may arise in DNA either because of its direct incorporation (against A in the template) or because of cytosine deamination. Mycobacteria with G, C rich genomes are inherently at high risk of cytosine deamination. Uracil DNA glycosylase activity is thus important for the survival of mycobacteria. A limitation in evaluating the druggability of this enzyme, however, is the absence of a rapid assay to evaluate catalytic activity that can be scaled for medium to high-throughput screening of inhibitors. Here we report a fluorescence-based method to assay uracil DNA glycosylase activity. A hairpin DNA oligomer with a fluorophore at its 5′ end and a quencher at its 3′ ends was designed incorporating five consecutive U:A base pairs immediately after the first base pair (5′ C:G 3’) at the top of the hairpin stem. Enzyme assays performed using this fluorescent substrate were seen to be highly sensitive thus enabling investigation of the real time kinetics of uracil excision. Here we present data that demonstrate the feasibility of using this assay to screen for inhibitors of Mycobacterium tuberculosis uracil DNA glycosylase. We note that this assay is suitable for high-throughput screening of compound libraries for uracil DNA glycosylase inhibitors.

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A novel molecular beacon based fluorescent method to assay uracil DNA glycosylase (UDG) activity has been developed.

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The single step assay is useful to determine real-time kinetics of uracil release.

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The assay is useful for high throughput screening of uracil DNA glycosylase inhibitors.

Advances in deep eutectic solvents and water: applications in metal- and biocatalyzed processes, in the synthesis of APIs, and other biologically active compounds

This review highlights recent advances in metal- and biocatalyzed transformations, in the synthesis of APIs and other biologically active compounds, when employing deep eutectic solvents and water as environmentally responsible solvents.

Unlocking Access to Enantiopure Fused Uracils by Chemodivergent [4+2] Cross-Cycloadditions: DFT-Supported Homo-Synergistic Organocatalytic Approach

The discovery of chemical methods enabling the construction of carbocycle-fused uracils which embody a three-dimensional and functional-group-rich architecture is a useful tool in medicinal chemistry oriented synthesis. In this work, an unprecedented amine-catalyzed [4+2] cross-cycloaddition is documented; it involves remotely enolizable 6-methyluracil-5-carbaldehydes and β-aryl enals, and chemoselectively produces two novel bicyclic and tricyclic fused uracil chemotypes in good yields with a maximum level of enantiocontrol. In-depth mechanistic investigations and control experiments support an intriguing homo-synergistic organocatalytic approach, where the same amine organocatalyst concomitantly engages both aldehyde partners in a stepwise eliminative [4+2] cycloaddition, whose vinylogous iminium ion intermediate product may diverge-depending upon conditions-to either bicyclic targets by hydrolysis or tricyclic products by a second homo-synergistic trienamine-mediated stepwise [4+2] cycloaddition.

5,5-Di-chloro-6-hy-droxy-dihydro-pyrimidine-2,4(1H,3H)-dione: mol-ecular and crystal structure, Hirshfeld surface analysis and the new route for synthesis with Mg(ReO4)2 as a new catalyst

The mol-ecular and crystal structures of the title compound, C4H4Cl2N2O3, were investigated by single-crystal X-ray diffraction and a Hirshfeld surface analysis. The title compound was synthesized by a new type of reaction using Mg(ReO4)2 as a new catalyst and a possible mechanism for this reaction is proposed. The six-membered ring adopts a half-chair conformation. In the crystal, hydrogen bonds connect the mol-ecules into double layers, which are connected to each other by halogen bonds. The Hirshfeld surface analysis revealed that the most important contributions for the crystal packing are from O⋯H/H⋯O (35.8%), Cl⋯Cl (19.6%), Cl⋯H/H⋯Cl (17.0%), H⋯H (8.3%), C⋯O/O⋯C (4.3%), Cl⋯O/O⋯Cl (4.2%) and O⋯O (4.1%) contacts.

Therapeutic potential of uracil and its derivatives in countering pathogenic and physiological disorders

Uracil is one of the most notable pharmacophores in medicinal chemistry as the pyrimidine nucleobase forms an integral part of many commercial drugs. Though the name uracil is usually associated with cancer drugs, there are many uracil-based compounds which can treat different diseases when they are employed. So far, there has been no in-depth review concerning uracil drugs in the market, or in the different stages of clinical trials, including those approved or discontinued. The current work focuses on the importance of uracil and its derivatives in treating different diseases. The use of uracil compounds in treating viral infections, cancer, diabetic, thyroid and autosomal recessive disorders are discussed in the review. The mechanism of action of each uracil drug with emphasis on their structure and properties are discussed in detail. The targeted action of these drugs on sites or on the different stages of a disorder/pathogenic life cycle are also discussed. This review encompasses uracil drugs approved as well as those in development from the 1950's onwards. The utility of uracil in drug discovery and its association with a wide range of diseases is brought forth within this review to demonstrate its potential to a wider audience.

Metabolic and Lipidomic Profiling of Vegetable Juices Fermented with Various Probiotics

Fermented vegetable juices have gained attention due to their various beneficial effects on human health. In this study, we employed gas chromatography-mass spectrometry, direct infusion-mass spectrometry, and liquid chromatography-mass spectrometry to identify useful metabolites, lipids, and carotenoids in vegetable juice (VJ) fermented with Lactobacillus plantarum HY7712, Lactobacillus plantarum HY7715, Lactobacillus helveticus HY7801, and Bifidobacterium animalis ssp. lactis HY8002. A total of 41 metabolites, 24 lipids, and 4 carotenoids were detected in the fermented and non-fermented VJ (control). The lycopene, α-carotene, and β-carotene levels were higher in VJ fermented with L. plantarum strains (HY7712 and HY7715) than in the control. Proline content was also elevated in VJ fermented with HY7715. Uracil, succinic acid, and α-carotene concentration was increased in VJ fermented with HY7801, while glycine and lycopene levels were raised in VJ fermented with HY8002. This study confirmed that each probiotic strain has distinctive characteristics and produces unique changes to metabolic profiles of VJ during fermentation. Our results suggest that probiotic-fermented VJ is a promising functional beverage that contains more beneficial metabolites and carotenoids than commercial non-fermented VJ.

The synthesis and biological evaluation of nucleobases/tetrazole hybrid compounds: A new class of phosphodiesterase type 3 (PDE3) inhibitors

Spired by the chemical structure of Cilostazol, a selective phosphodiesterase 3A (PDE3A) inhibitor, several novel hybrid compounds of nucleobases (uracil, 6-azauracil, 2-thiuracil, adenine, guanine, theophylline and theobromine) and tetrazole were designed and successfully synthesized and their inhibitory effects on PDE3A as well as their cytotoxicity on HeLa and MCF-7 cancerous cell lines were studied. Obtained results show the linear correlation between the inhibitory effect of synthesized compounds and their cytotoxicity. In some cases, the PDE3A inhibitory effects of synthesized compounds are higher than the Cilostazol. Besides, compared to a standard anticancer drug methotrexate, some of the synthesized compounds showed the higher cytotoxicity against the HeLa and MCF-7 cancerous cell lines.

In silico molecular docking and in vitro antioxidant activity studies of novel α-aminophosphonates bearing 6-amino-1,3-dimethyl uracil

In the present study, a new series of α-Aminophosphonates bearing 6-amino-1,3-dimethyluracil was synthesized in good to excellent yields (78-95%) by one-pot, three-component reaction of 6-amino-1,3-dimethyluracil, aromatic aldehydes and diethylphosphite via Kabachnik-Fields reaction by using an eco-friendly Eaton's reagent. All the compounds were screened for in vitro antioxidant studies by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydrogen peroxide (H₂O₂) methods. Among the synthesized bioactive molecules, 4a, 4d, 4g, and 4h exhibited promising antioxidant activity compared with the standard drug Ascorbic acid. Furthermore, in order to support the biological results of the compounds, molecular docking studies were performed against Aromatase enzyme for four compounds which revealed that the compounds 4a, 4d, 4g, and 4h have significant binding modes, with docking scores of -8.6, -8.4, -8.1 and -8.1 respectively and the compound 4b specifically has equal dock score of -8.0 when compared with the standard drug Exemestane.

Design, Synthesis, and Evaluation of Novel 2-Methoxyestradiol Derivatives as Apoptotic Inducers Through an Intrinsic Apoptosis Pathway

In order to discover novel derivatives in the anti-tumor field, reported anti-tumor pharmacophores (uridine, uracil, and thymine) were combined with 2-methoxyestradiol, which has been characterized as having excellent biological properties in terms of anti-tumor activity. Thus, 20 hybrids were synthesized through etherification at the 17β-OH or 3-phenolic hydroxyl group of 2-methoxyestradiol, and evaluated for their biological activities against the human breast adenocarcinoma MCF-7 cell lines, human breast cancer MDA-MB-231 cell lines, and the normal human liver L-O2 cell lines. As a result, all the uridine derivatives and single-access derivatives of uracil/thymine possessed good anti-proliferative activity against tested tumor cells (half maximal inhibitory concentration values from 3.89 to 19.32 µM), while only one dual-access derivative (21b) of thymine possessed good anti-proliferative activity (half maximal inhibitory concentration ≈ 25 µM). Among them, the uridine derivative 11 and the single-access derivative of uracil 12a possessed good anti-proliferative selectivity against tested tumor cells. Furthermore, basic mechanism studies revealed that hybrids 11 and 12a could induce apoptosis in MCF-7 cells through mitochondrial pathway. These hybrids induced morphological changes in MCF-7 cells, causing mitochondrial depolarization. These two hybrids also had the following effects: arrest of the cell cycle at the G2 phase; up regulation of Apaf-1, Bax, and cytochrome c; down regulation of Bcl-2 and Bcl-xL for both mRNA and protein; and increase of the expression for caspase-8 and -9. Finally, apoptotic effector caspase-3 was increased, which eventually caused nuclear apoptosis at least through an intrinsic pathway in the mitochondria. Additionally, hybrids 11 and 12a could specifically bind to estradiol receptor alpha in a dose-dependent manner.

Tuning uracil derivatives for the AIE-based detection of pyrene at a nano-molar level: single-crystal X-ray structure and DFT support

Single crystal X-ray structurally characterized azo-uracil derivative (L) is explored for the selective detection of pyrene via aggregation-induced emission (AIE) with 99-fold fluorescence enhancement.

New Uracil Analogs with Exocyclic Methylidene Group as Potential Anticancer Agents

BACKGROUND

Hybrid molecules combining uracil skeleton with methylidene exo-cyclic group were designed in the search for novel anticancer drug candidates.

OBJECTIVE

Two series of racemic 5-methylidenedihydrouracils, either 1,3-disubstituted or 1,3,6-trisubstituted were synthesized and tested for their possible cytotoxic activity against two cancer cell lines (HL-60 and MCF-7) and two healthy cell lines (HUVEC and MCF-10A). The most cytotoxic analogs were re-synthesized as pure enantiomers. The analog designated as U-332 [(R)-3-(4-bromophenyl)-1-ethyl-5-methylidene-6-phenyldihydrouracil], which had a very low IC50 value in HL-60 cell line (0.77μM) and was the most selective towards cancer cells was chosen for further experiments on HL-60 cell line, in order to determine the possible mechanism involved in its antineoplastic action.

METHODS

Cytotoxic activities of compound was assessed by the MTT assay. In order to explore the mechanism of U-332 activity, we performed quantitative real-time PCR analysis of p53 and p21 genes. Apoptosis, cell proliferation and DNA damage in HL-60 cells were determined using the flow cytometry. The ability of U-332 to determine GADD45ɑ protein level in HL-60 cells incubated with U-332 was analyzed by ELISA test.

RESULTS

U-332 was shown to generate excessive DNA damage (70% of the cell population), leading to p53 activation, resulting in p21 down-regulation and a significant increase of GADD45α protein, responsible for the cell cycle arrest in G2/M phase.

CONCLUSION

U-332 can be used as a potential lead compound in the further development of novel uracil analogs as anticancer agents.

Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: kinetic and computational studies

Acetylcholinesterase (AChE) and Butyrylcholinesterase (BuChE) inhibitors are interesting compounds for different therapeutic applications, among which Alzheimer's disease. Here, we investigated the inhibition of these cholinesterases with uracil derivatives. The mechanism of inhibition of these enzymes was observed to be due to obstruction of the active site entrance by the inhibitors scaffold. Molecular docking and molecular dynamics (MD) simulations demonstrated the possible key interactions between the studied ligands and amino acid residues at different regions of the active sites of AChE and BuChE. Being diverse of the classical AChE and BuChE inhibitors, the investigated uracil derivatives may be used as lead molecules for designing new therapeutically effective enzyme inhibitors.

Critical evaluation of current Alzheimer's drug discovery (2018-19) & futuristic Alzheimer drug model approach

Alzheimer's disease (AD), a neurodegenerative disease responsible for death of millions of people worldwide is a progressive clinical disorder which causes neurons to degenerate and ultimately die. It is one of the common causes of dementia wherein a person's incapability to independently think, behave and decline in social skills can be quoted as major symptoms. However the early signs include the simple non-clinical symptoms such as forgetting recent events and conversations. Onset of these symptoms leads to worsened conditions wherein the AD patient suffers severe memory impairment and eventually becomes unable to work out everyday tasks. Even though there is no complete cure for AD, rigorous research has been going on to reduce the progress of AD. Currently, a very few clinical drugs are prevailing for AD treatment. So this is the need of hour to design, develop and discovery of novel anti-AD drugs. The main factors for the cause of AD according to scientific research reveals structural changes in brain proteins such as beta amyloid, tau proteins into plaques and tangles respectively. The abnormal proteins distort the neurons. Despite the high potencies of the synthesized molecules; they could not get on the clinical tests up to human usage. In this review article, the recent research carried out with respect to inhibition of AChE, BuChE, NO, BACE1, MAOs, Aβ, H3R, DAPK, CSF1R, 5-HT4R, PDE, σ₁R and GSK-3β is compiled and organized. The summary is focused mainly on cholinesterases, Aβ, BACE1 and MAOs classes of potential inhibitors. The review also covers structure activity relationship of most potent compounds of each class of inhibitors alongside redesign and remodeling of the most significant inhibitors in order to expect cutting edge inhibitory properties towards AD. Alongside the molecular docking studies of the some final compounds are discussed.

Synthesis of d-glyco-alkynone derivatives via carbonylative Sonogashira reaction

A carbonylative Sonogashira coupling approach to the synthesis of glyco-alkynones is described. Eighteen examples were obtained in moderate do nearly quantitative yields under mild conditions employing Mo(CO)6 as a safe carbon monoxide source. Functionalization of the alkynyl moiety via cycloaddition with organic azides provided six examples of glyco-triazoles.