Uracil Moiety Research Articles

Manganese-oxidizing bacteria form multiple cylindrospermopsin transformation products with reduced human liver cell toxicity

Cylindrospermopsin (CYN) is a toxic alkaloid highly persistent in aquatic environments. Biological removal of CYN was described previously. However, no transformation products formed by biological processes could be identified so far. Here, we describe that various manganese-oxidizing bacteria (MOB) transform CYN completely at an initial mean concentration of 7 mg L−1 (17 μM) within 3 to 34 days. Regardless of the strain, and transformation rate, transformation of CYN by MOB led to the same seven transformation products identified by mass spectrometry, which suggests that the removal of CYN by MOB follows a similar mechanism. Oxidation was the main transformation process, and the uracil moiety was the most susceptible part of the CYN molecule. In vitro cytotoxicity tests with the transformation products of CYN formed by one of the tested strains against the two human liver cell lines HepG2 and HepaRG, revealed that the transformation products were substantially less toxic than pure CYN for both cell lines. The results suggest that incubation with MOB might be an option for water treatment to remove CYN and may allow more detailed studies on the fate of CYN in the environment.

Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach

"Mother nature" utilizes molecular self-assembly as an efficient tool to design several fascinating supramolecular architectures from simple building blocks like amino acids, peptides, and nucleobases. The self-assembling behavior of various biologically important molecules, morphological outcomes, molecular mechanism of association, and finally their applications in the real world draw broad interest from chemical and biological point of views. In this present Feature Article, the amyloid hypothesis is extended to include nonproteinaceous single metabolites that invoke a new paradigm for the pathology of inborn metabolic disorders. In this scenario, we dedicate this paper to understanding the morphological consequences and mechanistic insight of the self-assembly of some important amino acids (e.g., l-phenylalanine, l-tyrosine, glycine, etc.) and nucleobases (adenine and eight uracil moiety derivatives). Using proper spectroscopic and microscopic tools, distinct assembling mechanisms of different amino acids and nucleobases have been established. Again, lanthanides, polyphenolic compounds such as crown ethers, and a worldwide drink, beer, are elegantly employed as inhibitors of the resulting fibrillar aggregated structures. As a consequence, this study will cover literally a vast region in the self-assembling outcomes of single biologically important molecules, and therefore, we expect that a detailed understanding of such morphological outcomes using spectroscopic and microscopic approaches may open a new paradigm in this burgeoning field.

Hydration of Nucleobase as Probed by Electron Emission of Uridine-5′-Mono-Phosphate (UMP) in Aqueous Solution Induced by Nitrogen K-Shell Ionization

To identify the precise early radiation processes of DNA lesions, we measure electron kinetic energy spectra emitted from uridine-5′ monophosphate (UMP) in aqueous solution for the photoionization of the N 1s orbital electron and for the following Auger effect using a monochromatic soft X-ray synchrotron radiation at energies above the nitrogen K-shell ionization threshold. The change of photoelectron spectra for UMP in aqueous solutions at different proton concentrations (pH = 7.5 and 11.3) is ascribed to the chemical shift of the N3 nitrogen atom in uracil moiety of canonical and deprotonated forms. The lowest double ionization potentials for aqueous UMP at different pH obtained from the Auger electron spectra following the N 1s photoionization values show the electrostatic aqueous interaction of uracil moiety of canonical (neutral) and deprotonated (negatively charged) forms with hydrated water molecules.

Structure-Based Virtual Screening of Pseudomonas aeruginosa LpxA Inhibitors Using Pharmacophore-Based Approach.

Multidrug resistance in Pseudomonas aeruginosa is a noticeable and ongoing major obstacle for inhibitor design. In P. aeruginosa, uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) acetyltransferase (PaLpxA) is an essential enzyme of lipid A biosynthesis and an attractive drug target. PaLpxA is a homotrimer, and the binding pocket for its substrate, UDP-GlcNAc, is positioned between the monomer A–monomer B interface. The uracil moiety binds at one monomer A, the GlcNAc moiety binds at another monomer B, and a diphosphate form bonds with both monomers. The catalytic residues are conserved and display a similar catalytic mechanism across orthologs, but some distinctions exist between pocket sizes, residue differences, substrate positioning and specificity. The analysis of diversified pockets, volumes, and ligand positions was determined between orthologues that could aid in selective inhibitor development. Thenceforth, a complex-based pharmacophore model was generated and subjected to virtual screening to identify compounds with similar pharmacophoric properties. Docking and general Born-volume integral (GBVI) studies demonstrated 10 best lead compounds with selective inhibition properties with essential residues in the pocket. For biological access, these scaffolds complied with the Lipinski rule, no toxicity and drug likeness properties, and were considered as lead compounds. Hence, these scaffolds could be helpful for the development of potential selective PaLpxA inhibitors.

Structural Basis of the Substrate Selectivity of Viperin.

Viperin is a radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication by converting cytidine triphosphate (CTP) into 3'-deoxy-3',4'-didehydro-CTP and by additional undefined mechanisms operating through its N- and C-terminal domains. Here, we describe crystal structures of viperin bound to a SAM analogue and CTP or uridine triphosphate (UTP) and report kinetic parameters for viperin-catalyzed reactions with CTP or UTP as substrates. Viperin orients the C4' hydrogen atom of CTP and UTP similarly for abstraction by a 5'-deoxyadenosyl radical, but the uracil moiety introduces unfavorable interactions that prevent tight binding of UTP. Consistently, kcat is similar for CTP and UTP whereas the Km for UTP is much greater. The structures also show that nucleotide binding results in ordering of the C-terminal tail and reveal that this region contains a P-loop that binds the γ-phosphate of the bound nucleotide. Collectively, the results explain the selectivity for CTP and reveal a structural role for the C-terminal tail in binding CTP and UTP.

A bioinspired metal-organic approach to cross-linked functional 3D nanofibrous hydro- and aero-gels with effective mixture separation of nucleobases by molecular recognition.

The direct reaction between Cu(CH3COO)2 and uracil-1-acetic acid in water gives rise to the formation of a hydrogel consisting of entangled nanometric ribbons of a crystalline antiferromagnetic 1D Cu(ii) coordination polymer (CP) decorated with biocompatible uracil nucleobases. This hydrogel is the precursor for the preparation of a meso/macroporous ultralight aerogel that shows a remarkable Young's modulus. As a proof-of-concept of the molecular recognition capability of the terminal uracil moieties anchored at Cu(ii) CP chains, this material has been tested as the selective stationary phase for the separation of nucleobase derivatives in HPLC columns.

Synthesis of Uracil-Iodonium(III) Salts for Practical Utilization as Nucleobase Synthetic Modules.

Iodonium(III) salts bearing uracil moieties have recently appeared in the literature, but their structural scope and utilization are limited because of their hygroscopic characteristics. In this study, we describe our detailed investigations for synthesizing a series of uracil iodonium(III) salts derived with various structural motifs and counterions. These new compounds have been utilized as attractive synthetic modules in constructing functionalized nucleobase and nucleosides.

Anticancer evaluation of ruthenium(III) complexes with N-donor ligands tethered to coumarin or uracil moieties

In this study, the synthesis and characterization of new paramagnetic ruthenium(III) complexes: cis-[RuCl2(urdpa)] (1) {Hurdpa = 6-((bis(pyridin-2-ylmethyl)amino)methyl)uracil} and fac-[RuCl3(chrdpa)] (2) {chrdpa = 4-((bis(pyridin-2-ylmethyl)amino)methyl)-7-methoxycoumarin} are reported. These metal complexes have been comprehensively characterized by an array of physicochemical techniques and the X-ray solid-state structures of 1 and Hurdpa have been attained. Electronic spectroscopy Calf-Thymus DNA titrations revealed that both 1 and 2 are groove binders while molecular docking calculations indicated that the ligands’ steric factors dictate the mode of interaction of these individual ruthenium(III) species. These mononuclear ruthenium compounds were screened against cervical and breast cancer cell lines and show activity in the high micromolar range.

Preparation of 2'-Deoxy-2'-spirocyclopropylcytidine via an Alternative Cyclopropanation Reaction.

Herein we report the preparation of 2'-deoxy-2'-spirocyclopropylcytidine via an alternative cyclopropanation reaction starting from γ-silyl tertiary alcohols. Activation of the hydroxyl function with thionyl chloride in the presence of 4-DMAP allows the ring-closing step under mild conditions. Participation of the uracil moiety in the cyclization step is proposed.

Discovery of pyrimidine nucleoside dual prodrugs and pyrazine nucleosides as novel anti-HCV agents.

To explore the application potential of dual prodrug strategies in the development of anti-HCV agents, a variety of sofosbuvir derivatives with modifications at the C4 or N3 position of the uracil moiety were designed and synthesized. Some compounds exhibited potent anti-HCV activities, such as 4e and 8a-8c with similar EC50 values (0.20-0.22 μM) comparative to that of sofosbuvir (EC50 = 0.18 μM) in a genotype 1b based replicon Huh-7 cell line. Moreover, 8b displayed a good human plasma stability profile, and was easily metabolized in human liver microsomes expectantly. On the other hand, aiming to discover novel anti-HCV nucleosides, pyrazin-2(1H)-one nucleosides and their phosphoramidate prodrugs were investigated. Several active compounds were discovered, such as 25e (EC50 = 7.3 μM) and S-29b (EC50 = 19.5 μM). This kind of nucleosides were interesting and would open a new avenue for the development of antiviral agents.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions.

We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.

Highly stable photosensitive supramolecular micelles for tunable, efficient controlled drug release

Simple fabrication and manipulation of multi-stimuli responsive supramolecular polymers based on multiple, self-complementary, hydrogen bond interactions with the desired self-assembly behavior and desirable micellar properties for effective drug delivery under physiological conditions remains a grand challenge. Herein, we successfully developed a dual light- and temperature-responsive uracil-based polymer, BU-PPG, that spontaneously self‐assembles to form micelle-shaped nanoparticles in phosphate-buffered saline (PBS) via supramolecular interactions between uracil moieties. The resulting micelles exhibited controlled light-sensitive photodimerization, a low critical micellization concentration, low cytotoxicity towards MCF-7 cells and tunable drug-loading capacity, as well as extremely high drug-entrapment stability in media containing serum. These features make BU-PPG micelles highly attractive as a potential candidate for safe, effective delivery of anticancer drugs. Importantly, when irradiated with UV light at 254 nm, the drug-loaded irradiated BU-PPG micelles could be easily tuned to obtain the desired phase transition temperature, remained highly stable under normal physiological conditions for prolonged periods of time, and rapidly released the encapsulated drug when the temperature was increased to 40 °C due to an efficient temperature-induced hydrophilic-hydrophobic phase transition. Collectively, these advantages suggest the newly developed BU-PPG supramolecular system may represent a promising new strategy towards the development of controlled release drug delivery systems.

Tryptophan 32 mediates SOD1 toxicity in a in vivo motor neuron model of ALS and is a promising target for small molecule therapeutics

SOD1 misfolding, toxic gain of function, and spread are proposed as a pathological basis of amyotrophic lateral sclerosis (ALS), but the nature of SOD1 toxicity has been difficult to elucidate. Uniquely in SOD1 proteins from humans and other primates, and rarely in other species, a tryptophan residue at position 32 (W32) is predicted to be solvent exposed and to participate in SOD1 misfolding. We hypothesized that W32 is influential in SOD1 acquiring toxicity, as it is known to be important in template-directed misfolding. We tested if W32 contributes to SOD1 cytotoxicity and if it is an appropriate drug target to ameliorate ALS-like neuromuscular deficits in a zebrafish model of motor neuron axon morphology and function (swimming). Embryos injected with human SOD1 variant with W32 substituted for a serine (SOD1W32S) had reduced motor neuron axonopathy and motor deficits compared to those injected with wildtype or disease-associated SOD1. A library of FDA-approved small molecules was ranked with virtual screening based on predicted binding to W32, and subsequently filtered for analogues using a pharmacophore model based on molecular features of the uracil moiety of a small molecule previously predicted to interact with W32 (5′-fluorouridine or 5’-FUrd). Along with testing 5’-FUrd and uridine, a lead candidate from this list was selected based on its lower toxicity and improved blood brain barrier penetrance; telbivudine significantly rescued SOD1 toxicity in a dose-dependent manner. The mechanisms whereby the small molecules ameliorated motor neuron phenotypes were specifically mediated through human SOD1 and its residue W32, because these therapeutics had no measurable impact on the effects of UBQLN4D90A, EtOH, or tryptophan-deficient human SOD1W32S. By substituting W32 for a more evolutionarily conserved residue (serine), we confirmed the significant influence of W32 on human SOD1 toxicity to motor neuron morphology and function; further, we performed pharmaceutical targeting of the W32 residue for rescuing SOD1 toxicity. This unique residue offers future novel insights into SOD1 stability and toxic gain of function, and therefore poses an potential target for drug therapy.

Light-Induced Conformational Change of Uracil-Anchored Polythiophene-Regulating Thermo-Responsiveness.

Tuning the electronic structure of a π-conjugated polymer from the responsive side chains is generally done to get desired optoelectronic properties, and it would be very fruitful when light is used as an exciting tool that can also affect the backbone chain conformation. For this purpose, polythiophene- g-poly-[ N-(6-methyluracilyl)- N, N-dimethylamino chloride]ethyl methacrylate (PTDU) is synthesized. On exposure to diffuse sunlight, the uracil moieties of the grafted chains cause the absorption maximum of PTDU solution to show gradual blue shift of 87 nm and a gradual blue shift of 46 nm in the emission maximum, quenching its fluorescence with time. These effects occur specifically at the absorption range of polythiophene (PT) chromophore on direct exposure of light of different wavelengths, and the optimum wavelength is found to be 420 nm. Impedance study suggests a decrease in charge transfer resistance upon exposure because of conformational change of PTDU. Theoretical study indicates that on exposure to visible light, uracil moieties move toward the backbone to facilitate photoinduced electron transfer between the PT and the uracil, attributing to the variation in optoelectronic properties. Morphological and light-scattering studies exhibit a decrease in particle size because of coiling of the PT backbone and squeezing of the grafted chain on light exposure. The transparent orange-colored PTDU solution becomes hazy with a hike in emission intensity on addition of sodium halides and becomes reversibly transparent or hazy on heating or cooling. The screening of cationic centers of PTDU by varying halide anion concentration tunes the phase transition temperature. Thus, the light-induced variation in the backbone conformation is responsible for tuning the optoelectronic properties and regulates the thermos-responsiveness of the PTDU solution in the presence of halide ions.

Protomer-Dependent Electronic Spectroscopy and Photochemistry of the Model Flavin Chromophore Alloxazine.

Flavin chromophores play key roles in a wide range of photoactive proteins, but key questions exist in relation to their fundamental spectroscopic and photochemical properties. In this work, we report the first gas-phase spectroscopy study of protonated alloxazine (AL∙H+), a model flavin chromophore. Laser photodissociation is employed across a wide range (2.34–5.64 eV) to obtain the electronic spectrum and characterize the photofragmentation pathways. By comparison to TDDFT quantum chemical calculations, the spectrum is assigned to two AL∙H+ protomers; an N5 (dominant) and O4 (minor) form. The protomers have distinctly different spectral profiles in the region above 4.8 eV due to the presence of a strong electronic transition for the O4 protomer corresponding to an electron-density shift from the benzene to uracil moiety. AL∙H+ photoexcitation leads to fragmentation via loss of HCN and HNCO (along with small molecules such as CO2 and H2O), but the photofragmentation patterns differ dramatically from those observed upon collision excitation of the ground electronic state. This reveals that fragmentation is occurring during the excited state lifetime. Finally, our results show that the N5 protomer is associated primarily with HNCO loss while the O4 protomer is associated with HCN loss, indicating that the ring-opening dynamics are dependent on the location of protonation in the ground-state molecule.

Synthesis and Preliminary Evaluation of Biological Activity of Glycoconjugates Analogues of Acyclic Uridine Derivatives.

Herein we present the methodology for obtaining glycosyltransferase inhibitors, analogues of natural enzyme substrates of donor-type: UDP-glucose and UDP-galactose. The synthesis concerned glycoconjugates, nucleoside analogues containing an acyclic ribose mimetic linked to a uracil moiety in their structure. The biological activity of the synthesised compounds was determined on the basis of their ability to inhibit the model enzyme action of β-1,4-galactosyltransferase from bovine milk. The obtained results allowed to expand and supplement the existing library of synthetic compounds that are able to regulate the biological activity of enzymes from the GT class.

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

ABSTRACTThis report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.

Spectroscopy, molecular modeling and anti-oxidant activity studies on novel conjugates containing indole and uracil moiety

Herein we describe our results on the synthesis and molecular modeling of new conjugates containing indole and uracil moiety. This group of compounds has been synthesized by the reaction of indole alkaloid - gramine with appropriate uracil (uracil, 2-thiouracil, 6-methyl-2-thiouracil, thymine, 6-methyluracil and barbituric acid) using DMF as solvent. The structures of all products were confirmed by spectroscopic (1H NMR, 13C NMR, and FT-IR) analysis, mass spectrometry (EI) and PM5 semiempirical methods. Moreover the protonation constants for investigated compounds were determined. The obtained conjugates were screened in vitro for antioxidant and haemolytic activities, as well as for the protective effects against 2,2′-azobis (2-methylpropionamidine) dihydrochloride (AAPH)-induced oxidative haemolysis of human erythrocytes.

Self-assembling behavior of pyrimidine analogues: Unveiling the factors behind morphological diversity

Studying the self-assembly of uracil derivatives has great importance in biochemistry and nanotechnology. Now, in order to architect unique and interesting nucleobase nanostructures, herein, we report a simple, yet robust uracil moiety based platform which is potentially capable to self-assemble into fibrils.The system is validated using eight uracil moiety derivatives and the effect is examined via fluorescence lifetime imaging microscopy (FLIM), field emission scanning electron microscopy (FESEM), steady state DCM fluorescence and fluorescence correlation spectroscopy (FCS).FLIM and FESEM give qualitative information regarding the fibril formation of different morphologies including string, rod, flower, needles etc. Steady state DCM fluorescence and FCS establish a quantitative estimation of the extent of fibril formation. The involvement of hydrogen bonding interaction between NH and CO groups in the fibrillar growth of 5-IU is evoked from the crystallographic study. Again, the key role of different functional groups behind the formation of fibrillar network is investigated through blocking the COO− group of orotic acid with lanthanides. Finally, esterification and N,N′-dimethylation exquisitely explore the role and priority of different groups in the fibril formation of pyrimidine analogues. The results may be useful for understanding the processes of self-assembly of the uracil derivatives and the rationalized design of the uracil based supramolecular structures with specific properties.

Dual Stimuli-Responsive Nucleobase-Functionalized Polymeric Systems as Efficient Tools for Manipulating Micellar Self-Assembly Behavior

Environmental stimuli-responsive nucleobase-functionalized supramolecular polymers, a combination of oligomeric polypropylene glycol segments as a thermosensitive element and hydrogen-bonded uracil as a photosensitive moiety, were successfully developed and undergo spontaneous self-assembly to form uniform nanosized micelles via self-complementary double hydrogen bonding interactions between the uracil moieties in an aqueous environment. These micelles exhibit unique properties such as dual thermo- and photoresponsiveness, controllable lower critical concentration solution temperature (LCST), photoreactivity, and morphological transformation, making them highly attractive for various applications. More importantly, phase transitions and morphological studies confirmed the LCST behavior, size, and shape of the micelles can be easily tuned by adjusting the concentration and duration of ultraviolet irradiation of samples in aqueous solution, indicating introduction of uracil molecules into a water-soluble po...