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

Selectivity modulation and its prediction in cyclofructan-6 phase for chaotropic ions

BACKGROUND

Modifying additives to alter the selectivity of a single stationary phase and solvent system is appealing in mixed-mode separations. Silica-bonded cyclofructan-6 uniquely binds with cations strongly in the presence of organic solvents and is hydrolytically stable. Perchlorate with inorganic and organic quaternary ammonium cations could adjust retention for molecules with carboxylic acids, sulfonic acids, and nitrogen-containing functional groups, which are common in pharmaceutically relevant molecules. Perchlorate salts of ammonium, lithium, tetrabutylammonium, and tetramethylammonium were assessed for their selectivity in acetonitrile-water eluent systems.

RESULTS

This study provides a mathematical route to accomplish complex selectivity alterations by simply varying the perchlorate counterions. Two predictive tests based on l2-norm and principal component analysis (PCA) were proposed to choose the most distinct perchlorate additive pair for 17 test probes in retention time-space. The l2-norm provides a faster approach to measure variation caused by eluent additives for probe analytes. Ammonium and tetrabutylammonium perchlorate salts showed the maximum "distance" between them. The eluent additives strongly affected the elution times of carboxylic and sulfonic acids, and neutrals were mildly altered. A concentration study on these two additives with probe analytes ruled out a simple ion exchange interaction and suggested a multimodal retention mechanism. All additives yielded high-efficiency separations expected of 2.7 μm core-shell particles.

SIGNIFICANCE

The proposed mathematical tests will assist chromatographers in selecting distinct eluent additives for different classes of separations during method development. The applicability of the eluent selection strategy has been shown with the separation of three different biologically important classes of molecules containing analytes like cocaine, amphetamine, tianeptine, serotonin, lorazepam, and 5-fluorouracil.

Harnessing the Efficiency of Twin Boron Nitride and Graphene Monolayers for Anticancer Drug Delivery: Insights from DFT

An extensive amount of research has been focused on the development of state-of-the-art methodologies for drug administration. In this study, we have utilized density functional theory (DFT) for assessing the ability of a Twin monolayer of boron nitride and graphene, i.e., Twin-BN and Twin-Gr monolayer, as a carrier for delivering four anticancer drugs (ACDs) 5-fluorouracil (5-FU), gemcitabine (GC), cyclophosphamide (CP), and mercaptopurine (6-MP). Also, the properties of all drug molecules along with the Twin-BN and Twin-Gr and the complex of the ACD-Twin-BN/Gr monolayer were investigated to explore the usefulness of the Twin-BN and Twin-Gr monolayer as ACD carrier. The interaction between the monolayers and ACDs confirmed that the adsorption is feasible as the adsorption energy ranged from -0.41 eV to -0.95 eV in the case of Twin-BN, while it ranged from -0.43 eV to -0.61 eV in the case of Twin-Gr. Additionally, the change in the band gap of the Twin-BN and Twin-Gr monolayers after the adsorption of ACDs was considerable. We can conclude that among both monolayers, Twin-BN can be utilized as a highly effective carrier for delivering ACDs. Our findings showed that the monolayer Twin-BN could be explored as a drug transporter for highly efficient carrying of the considered ACDs.

Multiple Binding Modes of Inhibitors to Human Carbonic Anhydrases: An Update on the Design of Isoform-Specific Modulators of Activity

Human carbonic anhydrases (hCAs) are widespread zinc enzymes that catalyze the hydration of CO2 to bicarbonate and a proton. Currently, 15 isoforms have been identified, of which only 12 are catalytically active. Given their involvement in numerous physiological and pathological processes, hCAs are recognized therapeutic targets for the development of inhibitors with biomedical applications. However, despite massive development efforts, very few of the presently available hCA inhibitors show selectivity for a specific isoform. X-ray crystallography is a very useful tool for the rational drug design of enzyme inhibitors. In 2012 we published in Chemical Reviews a highly cited review on hCA family (Alterio, V. et al. Chem Rev. 2012, 112, 4421-4468), analyzing about 300 crystallographic structures of hCA/inhibitor complexes and describing the different CA inhibition mechanisms existing up to that date. However, in the period 2012-2023, almost 700 new hCA/inhibitor complex structures have been deposited in the PDB and a large number of new inhibitor classes have been discovered. Based on these considerations, the aim of this Review is to give a comprehensive update of the structural aspects of hCA/inhibitor interactions covering the period 2012-2023 and to recapitulate how this information can be used for the rational design of more selective versions of such inhibitors.

Antibacterial profile and antiproliferative activities over human tumor cells of new silver(I) complexes containing two distinct trifluoromethyl uracil isomers

New silver(I) complexes of 5-(trifluoromethyl)uracil (5TFMU) and 6-(trifluoromethyl)uracil (6TFMU) isomers were synthesized, characterized, and evaluated as antibacterial and antiproliferative agents. Based on elemental and thermogravimetric analyses, the Ag-5TFMU and Ag-6TFMU species are formulated as AgC5H2F3N2O2 and Ag2C5HF3N2O2, respectively. Infrared and 13C solid-state nuclear magnetic resonance spectroscopies suggest coordination of the trifluoromethyluracil isomers to silver by both nitrogen and oxygen atoms. Confirmation of their structure and connectivity was achieved, in the absence of single crystals of suitable quality, by state-of-the-art structural powder diffraction methods. In Ag-5TFMU, the organic ligand is tridentate and two distinct metal coordination environments are found (linear AgN2 as well as C2v AgO4 geometries), whereas Ag-6TFMU contains a complex polymeric structure with tetradentate dianionic 6TFMU moieties and five distinct AgX2 (X = N, O) fragments, further stabilized by ancillary (longer) Ag…O contacts. These species presented modest activity over Gram-positive and Gram-negative bacterial strains, whereas Ag-6TFMU was active over a set of tumor cells, with the best activity over prostate (PC-3) and kidney cell lines and selectivity indices of 4.6 and 1.3, respectively. On the other hand, Ag-5TFMU was active over all considered tumor cells except MCF-7 (breast cancer). The best activity was found for PC-3 cells, but no selectivity was observed. The Ag-5TFMU and Ag-6TFMU species also reduced the proliferation of tongue squamous cell carcinoma cell lines SCC - 4 and SCC-15. Preliminary biophysical assays by circular dichroism suggest that the Ag-5TFMU complex interacts with DNA by intercalation, an effect not seen in Ag-6TFMU.

Effects and Related Mechanisms of Allelopathy of Ambrosia trifida's Pollens on Corn Pollens, Stigmas, and Yield

Ambrosia trifida, a worldwide malignant invasive weed, can inhibit corn seed germination, seedling growth, and yield through allelopathy. However, it is unclear whether it can inhibit activities of corn pollens and stigmas and, thus, decrease corn yield through allelopathy. Here, we studied the allelopathic effects and related mechanisms of A. trifida's pollens on corn pollens, stigmas, and yield. The aqueous extract of A. trifida's pollens significantly inhibited activities of corn pollens and stigmas. Treating corn pollens and/or stigmas with A. trifida's pollens or their aqueous extract significantly decreased corn fruiting. Four allelochemicals were identified from A. trifida's pollens, which could significantly inhibit activities of corn pollens and stigmas, especially isoquercetin and quercetin. These compounds could interact with five key enzymes in the respiratory metabolism of corn, inhibiting the activities of these enzymes and, thus, respiratory metabolism. Our study provides a new pathway and mechanism by which invasive plants affect crop yield.

Design, Synthesis, and Biological Studies of C-5-Substituted Diazenyl Derivatives of Uracil as Potent and Selective Antileishmanial Agents Targeting Uridine Biosynthesis Pathway Enzymes

Herein, we describe the design and synthesis of a series of C-5-substituted diazenyl derivatives of uracil, exhibiting selective and potent antileishmanial but not antibacterial or antifungal activity. The formation of the substituted derivatives was confirmed by using FTIR, 1H, 13C NMR, and HRMS analysis. Among all of the sets of tested compounds, only three [4a, 6b, and 8b] showed the highest activity against Leishmania donovani (LD) promastigote and amastigote models of LD infections. Further, the cytotoxicity assays performed using three different cell lines, Vero cells, J774 cells, and THP1 cells, along with erythrocyte hemolysis assay showed the highest biocompatibility for the 4a, making it a lead compound for further biological assays. The LD cell death associated with 4a was not linked with ergosterol depletion, a common mechanism of action of antileishmanial drugs like amphotericin B (AmB). However, the LD cell death in the presence of 4a was reversed significantly through supplementation of uridine monophosphate (UMP), indicating the specific role of uridine biosynthesis pathway as the target of 4a. Furthermore, the in silico studies predicted orotidine monophosphate decarboxylase enzyme (OMPDCase) from LD as the plausible target for 4a. The proteomics analysis showed stronger downregulation of the aforementioned OMPDCase and also for a few other enzymes that are involved in the UMP biosynthesis pathway. This indicates that OMPDCase and other enzymes that regulate the UMP biosynthesis may be the target of 4a. Overall, the C-5-substituted diazenyl derivatives of uracil are presented here as novel and potent antileishmanial agents that can be used for treating visceral leishmaniasis (VL) wherein at present drug resistance and side effects of existing drugs demand a look for safer alternatives.

Isocyanate-based multicomponent reactions

Since their discovery, multicomponent reactions have attracted significant attention due to their versatility and efficiency. This review aims to explore the latest advancements in isocyanate-based multicomponent reactions and the sophisticated chemical opportunities they present for generating molecules of interest. The added value of the methodologies described, supported by mechanism schemes, as well as scopes of application, will be discussed. These developments will be organised as the main accessible chemical functions and sorted according to their type of MCR (3, 4 or 5-MCR).

KOtBu-Promoted [4+2] Annulation-Dehydration Cascade Enabling the Construction of Diverse 2-Pyridone-Fused Uracils

A KOtBu-promoted [4+2] annulation-dehydration cascade reaction has been developed, enabling the efficient synthesis of diverse 2-pyridone-fused uracils through a vinylogous enolization strategy involving o-quinodimethane (oQDM) dienolate intermediates. This method provides a simple yet robust approach for constructing structurally interesting fused N-heterocycles that incorporate two privileged scaffolds, both of which are widely recognized in drug discovery. Consequently, these compounds hold significant potential for biological and pharmacological applications. Moreover, further transformations of the products obtained from this process allow access to highly functionalized and structurally diverse uracil derivatives, expanding the scope of accessible chemical diversity.

Development of a Divergent Synthesis Strategy for 5-Sulfonyl-Substituted Uracil Derivatives

An efficient, diversity-orientated synthesis of 5-sulfone-substituted uracils was established. The use of protecting groups to synthesize sulfones from N-heterocycles was avoided. Various heterocycles were synthesized for the first time from favorable, easily accessible starting materials. Diversity-orientated syntheses are important for the medicinal chemistry of virostatics and chemotherapeutics. This approach provides a broad substrate tolerance and excellent yields of up to 98%.

A rapid and scalable method for visible light induced bromination of uracil derivatives in a falling film looping photoreactor

Visible light induced green synthesis of 5-bromouracil derivatives using N-bromosuccinimide (NBS) in acetonitrile under batch operation with a constant photon flux of 46 μmol s-1 is reported. This methodology has shown excellent tolerance with various 6-substituted and N-substituted uracils and is also applicable for various pyrimidine and arene derivatives. The reaction proceeded through the formation of a bromine molecule via a radical pathway followed by an electrophilic substitution reaction, and this hybrid nature of the reaction pathway in the presence of light made the process faster. We successfully synthesized twenty-one derivatives and characterized them using various spectroscopic methods. Finally, the three different modules of the looping falling film reactor were used to show the successive scalability of the process with comparable photonic characteristics and reaction conditions. We achieved milligram to multigram scale reaction with almost equal efficiency and maximum productivity up to 1.2 kg per day.

Data-Driven Modelling of Substituted Pyrimidine and Uracil-Based Derivatives Validated with Newly Synthesized and Antiproliferative Evaluated Compounds

The pyrimidine heterocycle plays an important role in anticancer research. In particular, the pyrimidine derivative families of uracil show promise as structural scaffolds relevant to cervical cancer. This group of chemicals lacks data-driven machine learning quantitative structure-activity relationships (QSARs) that allow for generalization and predictive capabilities in the search for new active compounds. To achieve this, a dataset of pyrimidine and uracil compounds from ChEMBL were collected and curated. A workflow was developed for data-driven machine learning QSAR using an intuitive dataset design and forwards selection of molecular descriptors. The model was thoroughly externally validated against available data. Blind validation was also performed by synthesis and antiproliferative evaluation of new synthesized uracil-based and pyrimidine derivatives. The most active compound among new synthesized derivatives, 2,4,5-trisubstituted pyrimidine was predicted with the QSAR model with differences of 0.02 compared to experimentally tested activity.

Mechanochemical Regioselective [3+3] Annulation of 6-Amino Uracil with Propargyl Alcohols Catalyzed by a Brønsted Acid/Hexafluoroisopropanol

A mechanochemistry approach is developed for regioselective synthesis of functionalized dihydropyrido[2,3-d]pyrimidines by milling propargylic alcohols and 6-aminouracils with HFIP/p-TsOH. In the case of tert-propargyl alcohols, this [3+3] cascade annulation proceeded through allenylation of uracil followed by a 6-endo trig cyclization. With sec-propargyl alcohols, the reaction furnished the propargylation of uracil. This atom economy ball milling reaction allows access to a broad range of dihydropyrido[2,3-d]pyrimidine derivatives in excellent yields. We demonstrated the gram scale synthesis of 3 g and post-synthetic modifications to effect the cyclization of 5 to 6.

Phosphine-Catalyzed Synthesis and Cytotoxic Evaluation of Michael Adducts of the Sesquiterpene Lactone Arglabin

A general method for chemo- and diastereoselective modification of anticancer natural product arglabin with nitrogen- and carbon-centered pronucleophiles under the influence of nucleophilic phosphine catalysts was developed. The locked s-cis-geometry of α-methylene-γ-butyrolactone moiety of arglabin favors for the additional stabilization of the zwitterionic intermediate by electrostatic interaction between phosphonium and enolate oxygen centers, leading to the unprecedentedly high efficiency of the phosphine-catalyzed Michael additions to this sesquiterpene lactone. Using n-Bu3P as the catalyst, pyrazole, phthalimide, 2-oxazolidinone, 4-quinazolinone, uracil, thymine, cytosine, and adenine adducts of arglabin were obtained. The n-Bu3P-catalyzed reaction of arglabin with active methylene compounds resulted in the predominant formation of bisadducts bearing a new quaternary carbon center. All synthesized Michael adducts and previously obtained phosphorylated arglabin derivatives were evaluated in vitro against eleven cancer and two normal cell lines, and the results were compared to those of natural arglabin and its dimethylamino hydrochloride salt currently used as anticancer drugs. 2-Oxazolidinone, uracil, diethyl malonate, dibenzyl phosphonate, and diethyl cyanomethylphosphonate derivatives of arglabin exhibited more potent antiproliferative activity towards several cancer cell lines and lower cytotoxicity towards normal cell lines in comparison to the reference compounds, indicating the feasibility of the developed methodology for the design of novel anticancer drugs with better therapeutic potential.

1H-NMR Metabolomic Study of the Mushroom Pleurotus djamor for the Identification of Nematocidal Compounds

Due to the increasing populations of anthelmintic-resistant gastrointestinal nematodes and as a consequence of the adverse effects of synthetic drugs, this study focuses on the search for secondary metabolites with nematocidal activity from the edible mushroom Pleurotus djamor using The proton nuclear magnetic resonance (1H-NMR) metabolomics. The highest activity was shown by the ethyl acetate fractions of mycelium (EC50 290.8 µg/mL) and basidiomes (EC50 282.7 µg/mL). Principal component analysis (PCA) and hierarchical data analysis (HCA) of the 1H-NMR metabolic profiles data showed that the ethanolic extracts, the ethyl acetate, butanol, and water fractions from mycelium have different metabolic profiles than those from basidiomes, while low polarity (hexane) fractions from both stages of fungal development show similar profiles. Orthogonal partial least squares discriminant analysis (OPLS-DA) allowed the identification of signals in the 1H-NMR metabolic profile associated with nematocidal activity. The signals yielded via OPLS-DA and bidimensional NMR analysis allowed the identification of uracil as a component in the ethyl acetate fraction from basidiomes, with an EC50 of 237.7 µg/mL. The results obtained showed that chemometric analyses of the 1H-NMR metabolic profiles represent a viable strategy for the identification of bioactive compounds from samples with complex chemical profiles.

Reaction Pattern and Mechanistic Aspects of Iodine and Iodine-Based Reagents in Selenylation of Aliphatic, Aromatic, and (Hetero)Cyclic Systems

Organoselenium compounds have been the subject of extensive research since the discovery of the biologically active compound ebselen. Ebselen has recently been found to show activity against the main protease of the virus responsible for COVID-19. Other organoselenium compounds are also well-known for their diverse biological activities, with such compounds exhibiting interesting physical properties relevant to the fields of electronics, materials, and polymer chemistry. In addition, the incorporation of selenium into various organic molecules has garnered significant attention due to the potential of selenium to enhance the biological activity of these molecules, particularly in conjunction with bioactive heterocycles. Iodine and iodine-based reagents play a prominent role in the synthesis of organoselenium compounds, being valued for their cost-effectiveness, non-toxicity, and ease of handling. These reagents efficiently selenylate a broad range of organic substrates, encompassing alkenes, alkynes, and cyclic, aromatic, and heterocyclic molecules. They serve as catalysts, additives, inducers, and oxidizing agents, facilitating the introduction of different functional groups at alternate positions in the molecules, thereby allowing for regioselective and stereoselective approaches. Specific iodine reagents and their combinations can be tailored to follow the desired reaction pathways. Here, we present a comprehensive review of the progress in the selenylation of organic molecules using iodine reagents over the past decade, with a focus on reaction patterns, solvent effects, heating, microwave, and ultrasonic conditions. Detailed discussions on mechanistic aspects, such as electrophilic, nucleophilic, radical, electrochemical, and ring expansion reactions via selenylation, multiselenylation, and difunctionalization, are included. The review also highlights the formation of various cyclic, heterocyclic, and heteroarenes resulting from the in situ generation of selenium intermediates, encompassing cyclic ketones, cyclic ethers, cyclic lactones, selenophenes, chromones, pyrazolines, pyrrolidines, piperidines, indolines, oxazolines, isooxazolines, lactones, dihydrofurans, and isoxazolidines. To enhance the reader's interest, the review is structured into different sections covering the selenylation of aliphatic sp2/sp carbon and cyclic sp2 carbon, and then is further subdivided into various heterocyclic molecules.

Metabolomics analysis of okara probiotic beverages fermented with Lactobacillus gasseri and Limosilactobacillus fermentum by LC-QTOF-MS/MS

In this study, okara was fermented with probiotic strains Lactobacillus gasseri LAC 343 and Limosilactobacillus fermentum PCC, respectively. Significant increases in cell count (by 2.22 log CFU/mL for LAC and 0.82 log CFU/mL for PCC) and significant decreases in pH (by 1.31 for LAC and 1.03 for PCC) were found in fermented okara slurry. In addition, strain LAC tended to produce amino acids, while strain PCC depleted most amino acids. An untargeted metabolomic-based approach using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to further understand the compositional changes and potential health benefits by identifying bioactive metabolites in fermented okara slurry. We successfully identified various beneficial bioactive compounds including γ-aminobutyric acid, indolelactic acid, d-phenyllactic acid, and p-hydroxyphenyllactic acid which had differences in fold-changes in okara slurry fermented with different strains. Our study indicated the feasibility of using probiotics to ferment okara for novel functional food development.

2-Thioxo-3,4-dihydropyrimidine and thiourea endowed with sulfonamide moieties as dual EGFRT790M and VEGFR-2 inhibitors: Design, synthesis, docking, and anticancer evaluations

The effectiveness of a new series of thiopyrimidine and thiourea containing sulfonamides moieties was tested on HCT-116, MCF-7, HepG2, and A549. HepG2 cell line was the one that all the new derivatives affected the most. The greatest potent compounds against the four HepG2, HCT116, MCF-7, and A549 cell lines were 8f and 8g with IC50  = 4.13, 6.64, 5.74, 6.85 µM and 4.09, 4.36, 4.22, 7.25 µM correspondingly. Compound 8g exhibited higher activity than sorafenib against HCT116 and MCF-7 but exhibited lower activity against HepG2 and A549. Moreover, compounds 8f and 8g exhibited higher activities than erlotinib on HepG2, HCT116, and MCF-7 but demonstrated lower activity on A549. The most potent cytotoxic derivatives 6f, 6g, 8c, 8d, 8e, 8f, and 8g were examined on normal VERO cell lines. Our derivatives have low toxicity on VERO cells with IC50 values ranging from 32.05 to 53.15 μM. Additionally, all compounds were assessed for dual VEGFR-2 and EGFRT790M inhibition effects. Compounds 8f and 8g were the most potent derivatives inhibited VEGFR-2 at IC50 value of 0.88 and 0.90 µM, correspondingly. As well, derivatives 8f and 8g could inhibit EGFRT790M demonstrating strongest effects with IC50  = 0.32 and 0.33 µM sequentially. Additionally, the greatest active derivatives ADMET profile was evaluated in relationship with sorafenib and erlotinib as reference agents. The data attained from docking were greatly related to that achieved from the biological testing.

BODIPY-fused uracil: synthesis, photophysical properties, and applications

Fluorescent nucleobase and nucleic acid analogs are important tools in chemical and molecular biology as fluorescent labelling of nucleobases has applications in cellular imaging and anti-tumor activity. Boron-dipyrromethene (BODIPY) dyes exhibiting high brightness and good photostability are extensively used as fluorescent labelling agents and as type II photosensitizers for photodynamic therapy. Thus, the combination of nucleobases and BODIPY to obtain new compounds with both anti-tumor activity and fluorescent imaging functions is the focus of our research. We synthesized two new nucleobase analogs 1 and 2 by fusing the BODIPY core directly with uracil which resulted in favorable photophysical properties and high emission quantum efficiencies particularly in organic solvents. Further, we explored the newly synthesized derivatives, which possessed good singlet oxygen generation efficiencies and bio-compatibility, as potential PDT agents and our results show that they exhibit in vitro anti-tumor activities.

Synthesis and biological evaluation of novel salicylidene uracils: Cytotoxic activity on human cancer cell lines and inhibitory action on enzymatic activity

A series of salicylidene uracil (1-18) derived from 5-aminouracil and substituted salicylaldehydes were analyzed for cytotoxic activity and enzyme inhibitory potency. Nine out of eighteen derivatives (6-8, 10, 12-15, 18) are novel molecules synthesized for the first time in this work, and other derivatives were previously synthesized by our group. The compounds were characterized by Proton nuclear magnetic resonance, carbon nuclear magnetic resonance, fourier transform infrared spectroscopy, and elemental analysis. All compounds were tested for their in vitro cytotoxicity against PC-3 (human prostate adenocarcinoma), A549 (human alveolar adenocarcinoma), and SHSY-5Y (human neuroblastoma) cancer cell lines and the nontumorigenic HEK293 (human embryonic kidney cells) cell line. The 3,5-di-tert-butylsalicylaldehyde derived compound (8) was toxic to PC-3 human prostate adenocarcinoma cells, showing a promising IC50 value at 7.05 ± 0.76 μM. The present study also aimed to evaluate the inhibitory effects of the compounds against several key enzymes, namely carbonic anhydrase I and II (CA I and CA II), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and glutathione reductase (GR), which are implicated in various global disorders, such as Alzheimer's disease, epilepsy, cancer, malaria, diabetes, and glaucoma. The inhibitory profiles of the tested compounds were assessed by determining their Ki values, which ranged from 2.96 to 9.24 nM for AChE, 3.78 to 12.57 nM for BChE, 8.42 to 25.74 nM for CA I, 7.24 to 19.74 nM for CA II, and 0.541 to 1.124 μM for GR. Molecular docking studies were also performed for all compounds. Most derivatives exhibited much more effective inhibitory action compared with clinically used standards. Thus, our findings indicate that the salicylidene derivatives presented in this study are promising drug candidates that need further evaluation.

Medicinal chemistry aspects of uracil containing dUTPase inhibitors targeting colorectal cancer

Deoxyuridine-5'-triphosphate nucleotidohydrolase (dUTPase), a vital enzyme in pyrimidine metabolism, is a prime target for treating colorectal cancer. Uracil shares structural traits with DNA/RNA bases, prompting exploration by medicinal chemists for pharmacological modifications. Some existing drugs, including thymidylate synthase (TS) and dUTPase inhibitors, incorporate uracil moieties. These derivatives hinder crucial cell proliferation pathways encompassing TS, dUTPases, dihydropyrimidine dehydrogenase, and uracil-DNA glycosylase. This review compiles uracil derivatives that have served as dUTPase inhibitors across various organisms, forming a library for targeting human dUTPase. Insights into their structural requisites for human applications and comparative analyses of binding pockets are provided for analyzing the compounds against human dUTPase.

Novel sofosbuvir derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective

The human coronavirus, SARS-CoV-2, had a negative impact on both the economy and human health, and the emerging resistant variants are an ongoing threat. One essential protein to target to prevent virus replication is the viral RNA-dependent RNA polymerase (RdRp). Sofosbuvir, a uridine nucleotide analog that potently inhibits viral polymerase, has been found to help treat SARS-CoV-2 patients. This work combines molecular docking and dynamics simulation (MDS) to test 14 sofosbuvir-based modifications against SARS-CoV-2 RdRp. The results reveal comparable (slightly better) average binding affinity of five modifications (compounds 3, 4, 11, 12, and 14) to the parent molecule, sofosbuvir. Compounds 3 and 4 show the best average binding affinities against SARS-CoV-2 RdRp (- 16.28 ± 5.69 and - 16.25 ± 5.78 kcal/mol average binding energy compared to - 16.20 ± 6.35 kcal/mol for sofosbuvir) calculated by Molecular Mechanics Generalized Born Surface Area (MM-GBSA) after MDS. The present study proposes compounds 3 and 4 as potential SARS-CoV-2 RdRp blockers, although this has yet to be proven experimentally.

Synthesis and Biological Evaluation of Novel Uracil Derivatives as Thymidylate Synthase Inhibitors

Cell division is driven by nucleic acid metabolism, and thymidylate synthase (TYMS) catalyzes a rate-limiting step in nucleotide synthesis. As a result, thymidylate synthase has emerged as a critical target in chemotherapy. 5-Fluorouracil (5-FU) is currently being used to treat a wide range of cancers, including breast, pancreatic, head and neck, colorectal, ovarian, and gastric cancers The objective of this study was to establish a new methodology for the low-cost, one-pot synthesis of uracil derivatives (UD-1 to UD-5) and to evaluate their therapeutic potential in BC cells. One-pot organic synthesis processes using a single solvent were used for the synthesis of drug analogues of Uracil. Integrated bioinformatics using GEPIA2, UALCAN, and KM plotter were utilized to study the expression pattern and prognostic significance of TYMS, the key target gene of 5-fluorouracil in breast cancer patients. Cell viability, cell proliferation, and colony formation assays were used as in vitro methods to validate the in silico lead obtained. BC patients showed high levels of thymidylate synthase, and high expression of thymidylate synthase was found associated with poor prognosis. In silico studies indicated that synthesized uracil derivatives have a high affinity for thymidylate synthase. Notably, the uracil derivatives dramatically inhibited the proliferation and colonization potential of BC cells in vitro. In conclusion, our study identified novel uracil derivatives as promising therapeutic options for breast cancer patients expressing the augmented levels of thymidylate synthase.

Unlocking the Potential of Deep Eutectic Solvents for C-H Activation and Cross-Coupling Reactions: A Review

Green chemistry principles have underpinned the development of deep eutectic solvents (DESs). In this brief overview, we discuss the potential of DESs as a greener alternative to volatile organic solvents for cross-coupling and C-H activation reactions in organic chemistry. DESs offer numerous benefits, such as easy preparation, low toxicity, high biodegradability, and the potential to replace volatile organic compounds. The ability of DESs to recover the catalyst-solvent system enhances their sustainability. This review highlights recent advances and challenges in utilizing DESs as a reaction media, as well as the impact of physicochemical properties on the reaction process. Several types of reactions are studied to highlight their effectiveness at promoting C-C bond formation. Aside from demonstrating the success of DESs in this context, this review also discusses the limitations and future prospects of DESs in organic chemistry.

Preparation and Characterization of a New Bis-Uracil Chitosan-Based Hydrogel as Efficient Adsorbent for Removal of Anionic Congo Red Dye

A new hydrogel, based on chitosan crosslinked with 2-chlorophenyl-bis(6-amino-1,3-dimethyluracil-5-yl) methane, (2Clph-BU-Cs), has been successfully created. Various instrumental techniques such as elemental analysis, FTIR, SEM, and XRD were used to prove its structure. Its removal efficiency for anionic Congo red (CR) dye under different conditions for industrial wastewater treatment was studied. For optimizing the conditions to maximize CR dye removal, the impacts of temperature, contact time, pH, and initial concentration of the dye on adsorption capacity were investigated. The removal of the dye was pH-dependent, with a much higher value achieved at pH 4 than at pH 7 and 9. The maximum adsorption capacity of the hydrogel was 93.46 mg g^-1. The model of adsorption process was fitted to the pseudo-second-order kinetic model. The intraparticle diffusion demonstrated the multi-step nature of the adsorption process. The thermodynamic results showed that the adsorption process was endothermic because of the positive value of enthalpy (43.70 kJ mol^-1). The process of adsorption at high temperatures was spontaneous, according to the values of ∆G⁰. An increase in randomness was seen in the value of ∆S°. Generally, the investigated hydrogel has the potential to be used as a promising effective reusable adsorbent for industrial wastewater remediation.

Advancements in Gold-Catalyzed Cascade Reactions to Access Carbocycles and Heterocycles: An Overview

This review summarizes recent developments (from 2006 to 2022) in numerous important and efficient carbo- and heterocycle generations using gold-catalyzed cascade protocols. Herein, methodologies involve selectivity, cost-effectiveness, and ease of product formation being controlled by the ligand as well as the counter anion, catalyst, substrate, and reaction conditions. Gold-catalyzed cascade reactions covered different strategies through the compilation of various approaches such as cyclization, hydroarylation, intermolecular and intramolecular cascade reactions, etc. This entitled reaction is also useful for the synthesis of spiro, fused, bridged carbo- and heterocycles.

Design, Synthesis, and Characterization of Novel Bis-Uracil Chitosan Hydrogels Modified with Zinc Oxide Nanoparticles for Boosting Their Antimicrobial Activity

A new series of hydrogels was successfully prepared by incorporating various substituted bisuracil (R-BU) linkages between chitosan Schiff's base chains (R-BU-CsSB) and between chitosan chains (R-BU-Cs). After protection of the amino groups of chitosan by benzaldehyde, yielding chitosan Schiff's base (CsSB), the reaction with epichlorohydrin was confined on the -OH on C6 to produce epoxy chitosan Schiff's base (ECsSB), which was reacted with R-BU to form R-BU-CsSB hydrogels, and finally, the bioactive amino groups of chitosan were restored to obtain R-BU-Cs hydrogels. Further, some R-BU-Cs-based ZnO nanoparticle (R-BU-Cs/ZnONPs) composites were also prepared. Appropriate techniques such as elemental analysis, FTIR, XRD, SEM, and EDX were used to verify their structures. Their inhibition potency against all the tested microbes were arranged as: ZnONPs bio-composites > R-BU-Cs hydrogels > R-BU-CsSB hydrogels > Cs. Their inhibition performance against Gram-positive bacteria was better than Gram-negative ones. Their minimum inhibitory concentration (MIC) values decreased as a function of the negative resonance effect of the substituents in the aryl ring of R-BU linkages in the hydrogels. Compared with Vancomycin, the ZnONPs bio-composites showed superior inhibitory effects against most of the tested Gram-negative bacteria, all inspected Gram-positive ones, and all investigated fungi.

Transition metal-catalyzed double Cvinyl-H bond activation: synthesis of conjugated dienes

Conjugated dienes have occupied a pivotal position in the field of synthetic organic chemistry and medicinal chemistry. They act as important synthons for the synthesis of various biologically important molecules and therefore, gain tremendous attention worldwide. A wide range of synthetic routes to access these versatile molecules have been developed in the past decades. Transition metal-catalyzed cross-dehydrogenative coupling (CDC) has emerged as one of the utmost front-line research areas in current synthetic organic chemistry due to its high atom economy, efficiency, and viability. In this review, an up-to-date summary including scope, limitations, mechanistic studies, stereoselectivities, and synthetic applications of transition metal-catalyzed double C_vinyl-H bond activation for the synthesis of conjugated dienes has been reported since 2013. The literature reports mentioned in this review have been classified into three different categories, i.e. (a) C_vinyl-C_vinyl bond formation via oxidative homo-coupling of terminal alkenes; (b) C_vinyl-C_vinyl bond formation via non-directed oxidative cross-coupling of linear/cyclic alkenes and terminal/internal alkenes, and (c) C_vinyl-C_vinyl bond formation via oxidative cross-coupling of directing group bearing alkenes and terminal/internal alkenes. Overall, this review aims to provide a concise overview of the current status of the considerable development in this field and is expected to stimulate further innovation and research in the future.

Synthesis of Novel Pyrimido[4,5-b] Quinolines Containing Benzyloxy and 1,2,3-Triazole Moieties by DABCO as a Basic Catalyst

DABCO was used as a basic and inexpensive catalyst for the synthesis of some new benzyloxy pyrimido[4,5-b]quinoline derivatives and 1,2,3- triazole-fused pyrimido[4,5-b]quinolines by the one-pot multi-component reaction of various benzyloxy benzaldehydes or benzylic -1,2,3-triazol-4-yl-methoxy benzaldehydes with dimedone and 6-amino-1,3-dimethyluracil at 90 °C under the solvent-free condition.

Design and synthesis of new thiazolidinone/uracil derivatives as antiproliferative agents targeting EGFR and/or BRAFV600E

Thiourea derivatives of uracil were efficiently synthesized via the reaction of 5-aminouracil with isothiocyanates. Then, we prepared uracil-containing thiazoles via condensation of thioureas with diethyl/dimethyl acetylenedicarboxylates. The structures of the products were confirmed by a combination of spectral techniques including infra-red (IR), nuclear magnetic resonance (NMR), mass spectrometry (MS) and elemental analyses. A rationale for the formation of the products is presented. The newly synthesized compounds were evaluated for their in vitro antiproliferative activity against four cancer cell lines. The compounds tested showed promising antiproliferative activity, with GI₅₀ values ranging from 1.10 µM to 10.00 µM. Compounds 3c, 5b, 5c, 5h, 5i, and 5j were the most potent derivatives, with GI₅₀ values ranging from 1.10 µM to 1.80 µM. Compound 5b showed potent inhibitory activity against EGFR and BRAF^V600E with IC₅₀ of 91 ± 07 and 93 ± 08 nM, respectively, indicating that this compound could serve as a dual inhibitor of EGFR and BRAF^V600E with promising antiproliferative properties. Docking computations revealed the great potency of compounds 5b and 5j towards EGFR and BRAF^V600E with docking scores of -8.3 and -9.7 kcal/mol and -8.2 and -9.3 kcal/mol, respectively.

Synthesis of 6-Methyluracilpentylviologen Resorcinarene Cavitand

Resorcinarenes, as macrocyclic compounds, are widely used to recognize substrates and create supramolecular assemblies. Their bowl-like form organizes functional groups at the upper and lower rims, which has a substantial impact on the molecular recognition of various substrates. As a result, resorcinarenes make good drug nanocarrier candidates. This paper presents the synthesis of a new resorcinarene cavitand functionalized along the upper rim with methyluracil and viologen fragments for its potential use in drug delivery. Methyluracils and viologens are well-known receptor-targeted compounds capable of facilitating the vector transfer of drugs and increasing the effectiveness of their action on cells. The paper describes the synthesis of resorcinarene modified with methyluracil and viologen groups along with its structure determined by 1H-, 13C-NMR and IR spectroscopy.

Intramolecular Interactions in Derivatives of Uracil Tautomers

The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/−OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer).

In Vitro Antioxidant and Pancreatic Anticancer Activity of Novel 5-Fluorouracil-Coumarin Conjugates

Molecular hybridization consists of the combination of two or more non-identical pharmacophores in a single molecule. It has emerged as a promising strategy that allows the design of molecular frameworks with enhanced activity and affinity compared to their parent drugs. In this work, two novel hybrids that combine the well-known anticancer chemotherapeutic agent 5-fluorouracil with antioxidant coumarin derivatives have been synthesized and characterized by means of a copper-catalyzed azide-alkyne cycloaddition (CuAAC). The conjugates showed good antioxidant properties and a high tendency to aggregate and form stable nanoparticles in aqueous media, with regular shape and uniform size. These materials have proven to be preferential cytotoxic agents in vitro against human pancreatic cancer cells PANC-1, with an activity superior to free 5-fluorouracil. These results open up the possibility of exploiting the synergistic combination between 5-fluorouracil and coumarin derivatives and warrant further investigation of these hybrids as promising pancreatic anticancer agents.

Uracil derivatives as HIV-1 capsid protein inhibitors: design, in silico, in vitro and cytotoxicity studies

A series of novel uracil derivatives such as bispyrimidine dione and tetrapyrimidine dione derivatives were designed based on the existing four-point pharmacophore model as effective HIV capsid protein inhibitors. The compounds were initially docked with an HIV capsid protein monomer to rationalize the ideas of design and to find the potential binding modes. The successful design and computational studies led to the synthesis of bispyrimidine dione and tetrapyrimidine dione derivatives from uracil and aromatic aldehydes in the presence of HCl using novel methodology. The in vitro evaluation in HIV p24 assay revealed five potential uracil derivatives with IC₅₀ values ranging from 191.5 μg ml⁻¹ to 62.5 μg ml⁻¹. The meta-chloro substituted uracil compound 9a showed promising activity with an IC₅₀ value of 62.5 μg ml⁻¹ which is well correlated with the computational studies. As expected, all the active compounds were noncytotoxic in BA/F3 and Mo7e cell lines highlighting the thoughtful design. The structure activity relationship indicates the position priority and lower log P values as the possible cause of inhibitory potential of the uracil compounds.

The paper describes the design, synthesis, computational and biological validation of a series of novel uracil derivatives as effective HIV capsid protein inhibitors.

A glutathione responsive nanocarrier based on viologen resorcinarene cavitand and 1-allylthymine

A glutathione-sensitive nanocarrier for doxorubicin to improve cellular penetration and selective cytotoxic effects on T98G human glioblastoma cells.

Visible-light-promoted sulfenylation of 6-aminouracils under catalyst-free conditions

Visible-light-promoted reactions have proven to be a decent strategy for the synthesis of complex molecules.

Cu-catalyzed C(sp2)-N-bond coupling of boronic acids and cyclic imides

A general Cu-catalyzed strategy for coupling cyclic imides and alkenylboronic acids by forming C(sp²)-N-bonds is reported. The method enables the practical and mild preparation of (E)-enimides. A large range of cyclic imides are allowed, and di- and tri-substituted alkenylboronic acids can be used. Full retention was observed in the configuration of the alkene double bond in the coupled products. The method is also applicable for preparing N-arylimides, using arylboronic acids as coupling partners. The usefulness of this strategy is exemplified by the convenient derivatization of the chemotherapy medication 5-flurouracil, the nucleoside uridine and the anti-epileptic drug phenytoin.

Unexpected Reaction Products of Uracil and Its Methyl Derivatives with Acetic Anhydride and Methylene Chloride

New acetyl derivatives of uracil, 6-methyluracil, and thymine were obtained in the course of an unconventional synthesis in methylene chloride. It was shown that products with the acetyloxymethyl fragment are formed according to a mechanism different from that for products with the acetyloxyethyl group. In particular, for uracil it was proven that the reaction with Ac₂O, TEA, and CH₂Cl₂ leads to 1-acetyloxymethyluracil, where the N¹ substituent is composed of the -CH₂- fragment that originated from CH₂Cl₂ and the 1-acetyloxy moiety from Ac₂O. The reaction of uracil with Ac₂O, TEA, CH₂Cl₂, and DMAP leads to an acetyloxyethyl derivative in which the -CH₂-CH₂- fragment originates from TEA and the 1-acetyloxy moiety from Ac₂O. A possible mechanism for the formation of new compounds was suggested and supported by the density functional theory/B3LYP quantum mechanical calculations. New compounds (39 in total, including seven deuterated) were fully characterized by nuclear magnetic resonance and high-resolution mass spectrometry techniques.

Coumarins and Gastrointestinal Cancer: A New Therapeutic Option?

Cancers of the gastrointestinal (GI) tract are often life-threatening malignancies, which can be a severe burden to the health care system. Globally, the mortality rate from gastrointestinal tumors has been increasing due to the lack of adequate diagnostic, prognostic, and therapeutic measures to combat these tumors. Coumarin is a natural product with remarkable antitumor activity, and it is widely found in various natural plant sources. Researchers have explored coumarin and its related derivatives to investigate their antitumor activity, and the potential molecular mechanisms involved. These mechanisms include hormone antagonists, alkylating agents, inhibitors of angiogenesis, inhibitors of topoisomerase, inducers of apoptosis, agents with antimitotic activity, telomerase inhibitors, inhibitors of human carbonic anhydrase, as well as other potential mechanisms. Consequently, drug design and discovery scientists and medicinal chemists have collaborated to identify new coumarin-related agents in order to produce more effective antitumor drugs against GI cancers. Herein, we summarize the therapeutic effects of coumarin and its derivatives against GI cancer.

Pyrimidine-2,4-dione targets STAT3 signaling pathway to induce cytotoxicity in hepatocellular carcinoma cells

Signal transducer and activator of transcription 3 (STAT3) is a tumorigenic transcription factor that is persistently activated in various human cancers including hepatocellular carcinoma (HCC). Therefore, STAT3 is considered as a prominent target to counteract the uncontrolled proliferation of cancer cells. In the present report, pyrimidine-2,4-diones (N-methyluracil derivatives) (MNK1-MNK14) were synthesized in an ionic liquid (BMIm PF₆) medium employing a ligand-free Suzuki-Miyaura cross-coupling process. Among the 14 derivatives, compound MNK8 showed good cytotoxicity towards both the tested cell lines and did not display a toxic effect against normal hepatocytes (LO2). MNK8 significantly increased the Sub-G1 cell count in both cell lines and the cytotoxic effect of MNK8 was found to be mediated through the suppression of constitutive phosphorylation of STAT3^Y705. It also decreased the DNA interaction ability of nuclear STAT3 in HCC cells. MNK8 downregulated the levels of apoptosis-related proteins (such as Bcl-2, cyclin D1, survivin) and increased cleaved caspase-3 inferring the apoptogenic effect of MNK8. It also reduced the CXCL12-triggered cell migration and invasion in in vitro assay systems. Overall, MNK8 has been demonstrated as a new inhibitor of STAT3 signaling cascade in HCC cells.

Coupling 6-chloro-3-methyluracil with copper: structural features, theoretical analysis, and biofunctional properties

As nucleobases in RNA and DNA, uracil and 5-methyluracil represent a recognized class of bioactive molecules and versatile ligands for coordination compounds with various biofunctional properties. In this study, 6-chloro-3-methyluracil (Hcmu) was used as an unexplored building block for the self-assembly generation of a new bioactive copper(II) complex, [Cu(cmu)₂(H₂O)₂]·4H₂O (1). This compound was isolated as a stable crystalline solid and fully characterized in solution and solid state by a variety of spectroscopic methods (UV-vis, EPR, fluorescence spectroscopy), cyclic voltammetry, X-ray diffraction, and DFT calculations. The structural, topological, H-bonding, and Hirshfeld surface features of 1 were also analyzed in detail. The compound 1 shows a distorted octahedral {CuN₂O₄} coordination environment with two trans cmu^- ligands adopting a bidentate N,O-coordination mode. The monocopper(II) molecular units participate in strong H-bonding interactions with water molecules of crystallization, leading to structural 0D → 3D extension into a 3D H-bonded network with a tfz-d topology. Molecular docking and ADME analysis as well as antibacterial and antioxidant activity studies were performed to assess the bioactivity of 1. In particular, this compound exhibits a prominent antibacterial effect against Gram negative (E. coli, P. aeruginosa) and positive (S. aureus, B. cereus) bacteria. The obtained copper(II) complex also represents the first structurally characterized coordination compound derived from 6-chloro-3-methyluracil, thus introducing this bioactive building block into a family of uracil metal complexes with notable biofunctional properties.

Novel triazole-sulfonamide bearing pyrimidine moieties with carbonic anhydrase inhibitory action: Design, synthesis, computational and enzyme inhibition studies

A series of new triazole-sulfonamide bearing pyrimidine derivatives were designed and synthesized via click chemistry. All new compounds (SH-1 to SH-28) were validated by ¹HNMR, ¹³CNMR, HRMS, and SH-3 was further structurally validated by X-Ray single diffraction study. These compounds (SH-1 to SH-28) were tested as inhibitors of human carbonic anhydrase (hCA) isoforms, such as hCA I, II, IX and XII, using a stopped flow CO₂ hydrase assay. Most of the compounds exhibited significant inhibitory activity against hCA II and weak inhibitory activity against hCA I. The target compounds also displayed moderate to excellent inhibitory activity against tumor-related hCAs IX and XII. Some compounds, e.g., SH-20 (K_i = 9.4 nM), SH-26 (K_i = 1.8 nM) and SH-28 (K_i = 0.82 nM) exhibited excellent inhibitory activity and selectivity profile against hCAs XII over IX. SH-23 displayed promising inhibitory activity and selectivity profile against both tumor-related hCAs IX (K_i = 2.9 nM) as well as XII (K_i = 0.82 nM) over hCA I and II. To understand the molecular interactions, molecular docking study of compounds SH-20, SH-23, SH-26 and SH-28 with hCA XII and SH-23 also with hCA IX were performed. The computational study evidenced favorable interaction between the inhibitors and active residues of both proteins. Some of these derivatives are promising leads for the development of selective, anticancer agents based on CA inhibitors.