Ureido Group Research Articles

Chirality Sensing of Chiral Carboxylic Acids by a Ureido-Linked Zinc Bisporphyrinate.

We designed and synthesized a ureido-linked zinc bisporphyrinate [Zn2(UBis)]. CD spectra show that this zinc bisporphyrinate has the ability to sense the chirality of chiral carboxylic acids without derivatization. Our studies suggest that the phenyl ring in the linker forms π-π interactions with porphyrin planes and that the carboxylic acid is coordinated to the zinc in the host-guest complex. DFT calculations show that the bisporphyrin adopts a "Z"-shaped configuration, and that the ureido group forms hydrogen bonds with carboxylic acids. The combination of π-π interactions, coordination interactions and hydrogen bonding interactions leads to the chirality sensing ability of [Zn2(UBis)].

PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains.

A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.

L-Citrullinato-Bipyridine and L-Citrullinato-Phenanthroline Mixed Copper Complexes: Synthesis, Characterization and Potential Anticancer Activity.

Citrulline (C6H13N3O3) is an amino acid found in the body as a zwitterion. This means its carboxylic and amine groups can act as Lewis donors to chelate metal cations. In addition, citrulline possesses a terminal ureido group on its aliphatic chain, which also appears to coordinate. Here, two new mixed complexes of citrulline were made with 1,10-phenanthroline and 2,2'-bipyridine. These compounds, once dissolved in water, gave aquo-complexes that were subject to DFT studies and in vitro toxicity studies on cancer cell lines (HeLa, MDA-MB-231, HCT 15, and MCF7) showed promising results. Docking studies with DNA were also conducted, indicating potential anticancer properties.

Molecular Environment Modulates CO2 Liberation from Carboxy-Biotin.

Carboxy-biotin serves as a coenzyme in certain carboxylases, exhibiting the remarkable capability to transfer a carboxy group to specific substrates. This process is made possible by the presence of biotin, a unique molecule that consists of a sulfur-containing tetrahydrothiophene ring fused to a ureido group. It is covalently attached to the enzyme via a flexible linker, allowing for its functionality. Biotin-dependent carboxylases consist of two distinct domains. The first domain (BC) facilitates biotin carboxylation by utilizing ATP, while the second domain (CT) transfers CO2 to the substrate. The process of ATP-dependent carboxylation using bicarbonate in the biotin carboxylase domain (BC) is well-known. However, the precise mechanism by which CO2 is released in the carboxyltransferase domain (CT) is still not fully understood. We employed advanced computational chemistry methods to investigate the decarboxylation process of carboxy-biotin in various molecular environments and different protonation states. Regardless of the polarity of the molecular surroundings, decarboxylation only occurs spontaneously in the protonated form. To determine the protonation state of biotin in different environments, we established an accurate computational chemistry method for calculating the pKa value of carboxy-biotin, reaching sub-kcal/mol accuracy. Based on our findings, nonpolar environments, such as the active site of the carboxyltransferase domain, have the ability to cause the spontaneous release of CO2 from carboxy-biotin. The CO2 release takes place spontaneously from protonated carboxy-biotin, promoting the carboxylation of substrates.

The chemistry of the Wender’s test for Dulcin

The reaction route of Wender’s test for Dulcin, p-phenetolecarbamide, is disclosed in this article. The many steps in this interesting oxido-degradation process are fully commented and the electron flow is given. Wender used fuming nitric acid as reagent. A violent reaction takes place; however, the test is safe due to the minute quantity employed of this sweetener. Further addition of phenol solution and sulphuric acid gives a blood-red colour. The reactions that occur are as follows: nitration of the ureido group, nitrous acid removal, nitrate formation, elimination of nitrous acid, nitroso group formation, separation of nitric acid and carbon monoxide, free radical degradation to p-benzoquinone imine, hydrolysis, and formation of red phenoquinone, the colour observed in the test.

Electro-Responsive Aggregation and Dissolution of Cationic Polymer Using Reversible Redox Reaction of Electron Mediator.

Stimuli-responsive aggregation of polymer chains in water has found a variety of applications in polymer science, biology, and chemical engineering. To date, the majority of the phase transitions between the aggregated and dissolved forms has been observed by changing the solution temperature, and an active and precise control on the phase transition with a high time resolution has been challenging. Herein, a reversible phase transition of poly(allylamine-co-allylurea) (PAU) in an aqueous electrolyte is achieved by electrochemical redox cycling of hexacyanoferrate(II/III) ([Fe(CN)6 ]4-/3- ) ion pair. The aggregation and dissolution cycle can be completed in a high-resolution time frame of as short as 5s. The strong electrostatic interaction between the protonated primary amino group of PAU and the tetravalent [Fe(CN)6 ]4- anion induces the aggregation, while the oxidation to the trivalent [Fe(CN)6 ]3- anion reduces the attractive force, and the polymer chain redissolves in solution. The ureido group of PAU helps the chain-folding process through the formation of inter/intrachain hydrogen-bonding networks, resulting in the sharp phase transition. By using [Fe(CN)6 ]4-/3- as the electron mediator, the electrochemical control on the large transparency change of polymer aqueous solution is realized for the first time.

On the mechanism of the Folin test for uric aci

The mechanism of the interaction of uric acid with sodium tungstate in phosphoric acid (Folin test) is described. This insight involves the following steps: addition of tungstic acid to the carbon-carbon double bond in uric acid. Protolysis of the organometallic ester gives rise to dihydroxyoxotungsten and an epoxide, via a concerted mechanism. Acid catalyzed ring opening of the oxirane produces a vicinal diol via reaction of the intermediate carbocation with water. Isomerization of the resulting carbinolamide groups is enhanced by the resonance of the ureido group. Breaking of the second carbinolamide gives urea and alloxan, 5-ketobarbituric acid hydrate. Uric acid oxidation in strong acidic medium like phosphoric acid produces alloxan, whereas oxidation in alkaline, neutral, or slightly acidic medium, gives allantoin.

Structure-activity relationship analysis of novel GSPT1 degraders based on benzotriazinone scaffold and its antitumor effect on xenograft mouse model

Molecular glue degraders, such as lenalidomide and pomalidomide, bind to cereblon (CRBN) E3 ligase and subsequently recruit neosubstrate proteins, Ikaros (IKZF1) and Aiolos (IKZF3), for the ubiquitination-proteasomal degradation process. In this study, we explored structure–activity relationship analysis for novel GSPT1 degraders utilizing a benzotriazinone scaffold previously discovered as a novel CRBN binder. In particular, we focused on the position of the ureido group on the benzotriazinone scaffold, substituent effect on the phenylureido group, and methyl substitution on the benzylic position of benzotriazinone. As a result, we identified 34f (TD-522), which exhibits strong anti-proliferative effects in both KG-1 (EC50 = 0.5 nM) and TMD-8 (EC50 = 5.2 nM) cell lines. Compound 34f effectively induced GSPT1 degradation with a DC50 of 0.269 nM and Dmax of >95 % at 10 nM concentration in KG-1 cells. An in vivo xenograft study showed that compound 34f effectively suppressed TMD8-driven tumor growth, suggesting a potential role in the development of novel GSPT1 degraders.

Structure-Activity Relationships for 5'' Modifications of 4,5-Aminoglycoside Antibiotics.

Modification at the 5''-position of 4,5-disubstituted aminoglycoside antibiotics (AGAs) to circumvent inactivation by aminoglycoside modifying enzymes (AMEs) is well known. Such modifications, however, unpredictably impact activity and affect target selectivity thereby hindering drug development. A survey of 5''-modifications of the 4,5-AGAs and the related 5-O-furanosyl apramycin derivatives is presented. In the neomycin and the apralog series, all modifications were well-tolerated, but other 4,5-AGAs require a hydrogen bonding group at the 5''-position for maintenance of antibacterial activity. The 5''-amino modification resulted in parent-like activity, but reduced selectivity against the human cytosolic decoding A site rendering this modification unfavorable in paromomycin, propylamycin, and ribostamycin. Installation of a 5''-formamido group and, to a lesser degree, a 5''-ureido group resulted in parent-like activity without loss of selectivity. These lessons will aid the design of next-generation AGAs capable of circumventing AME action while maintaining high antibacterial activity and target selectivity.

Naturally occurring ureidobromophenols with potent antioxidant activities from the marine red alga Rhodomela confervoides

An extensive investigation on the chemical components with potential antioxidant activity resulted in the characterization of four new ureidobromophenols (1–4) and two related metabolites (5 and 6) from ethyl acetate extract of the marine red alga Rhodomela confervoides. Their structures were determined using spectroscopic analysis and comparisons with known compounds. Compound 1 possesses unique structure of an ureido group bearing γ-butyric acid and 2,3-dibromo-4,5-dihydroxybenzyl moieties on the same nitrogen atom. Compounds 1–4 displayed significant antioxidant activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals with IC50 values ranging from 3.34 to 4.84 μM, which are more active than that of the positive controls ascorbic acid (IC50 = 20.1 μM) and butylated hydroxytoluene (IC50 = 82.1 μM). These compounds also exhibited potent activity against 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonate (ABTS) radicals with trolox equivalent antioxidant capacity (TEAC) values ranging from 3.25 to 5.01 mM, which are 3- to 5-fold potent than that of ascorbic acid (TEAC = 1.02 mM). The antioxidant activity of ureidobromophenols isolated from marine alga might boost the seaweed functional food ingredients or dietary food supplements in food industry.

Frontispiece: Urea Derivatives as Functional Molecules: Supramolecular Capsules, Supramolecular Polymers, Supramolecular Gels, Artificial Hosts, and Catalysts

The ideal hydrogen bonding ability of the ureido group leads to unique functions. In their review on page 5601, M. Yamanaka et al., summarize recent developments of urea derivatives that exhibit various functions: i) supramolecular capsules, ii) supramolecular polymers, iii) supramolecular gels, iv) artificial host molecules, and v) catalytic reactions.

Synthesis and Properties of 1,3-Disubstituted Ureas and Their Isosteric Analogs Containing Polycyclic Fragments: VII. Synthesis and Properties 1-[(Adamantan-1-yl)methyl]-3-(fluoro, chlorophenyl) Ureas

A series of 1,3-disubstituted ureas containing a lipophilic adamantane moiety tethered to the ureido group by a methylene bridge were synthesized by the reaction of 1-(isocyanatomethyl)adamantane with monohalo- and dihaloanilines in yields of up to 92%. The synthesized ureas are target oriented inhibitors of human soluble epoxide hydrolase (sEH).

Urea Derivatives as Functional Molecules: Supramolecular Capsules, Supramolecular Polymers, Supramolecular Gels, Artificial Hosts, and Catalysts.

Urea, which has both hydrogen bond acceptor and donor moieties, is an ideal structure for a supramolecular synthon. Various supramolecules having ureido group(s) have been widely developed. This article summarizes recent developments of urea derivatives that exhibit various functions: i) supramolecular capsules that form discrete urea-urea intermolecular hydrogen bonds, ii) supramolecular polymers that form continuous urea-urea intermolecular hydrogen bonds, iii) supramolecular gels that form continuous urea-urea intermolecular hydrogen bonds, iv) artificial host molecules based on the molecular recognition ability of the ureido group, and v) catalytic reactions developed by utilizing the molecular recognition ability of the ureido group.

Enantiomeric Separation of Chiral Triazole Pesticides by a mono-6-(4-Nitrophenyl)-ureido-β-cyclodextrin-Bonded Stationary Phase Using High-Performance Liquid Chromatography

A mono-6-(4-nitrophenyl)-ureido-β-cyclodextrin-bonded chiral stationary phase (NCDSP), containing π-electron withdrawing groups, was prepared by immobilizing a self-prepared mono-6-(4-nitrophenyl)-ureido-β-cyclodextrin ligand onto ordered mesoporous silica gel SBA-15, on which the ligand was synthesized by the reaction of mono-6-amino-β-cyclodextrin with 4-nitrophenylisocyanate. The structure of NCDSP was characterized by infrared spectroscopy, elemental analysis, thermogravimetric analysis and solid nuclear magnetic resonance. The introduction of electron-withdrawing (π-acidic) groups facilitated the separation of the π-electron-rich (π-basic) triazole chiral pesticides. In addition, the ureido group linkage allowed NCDSP to be a hydrogen bond-accepting and -donating chiral station phase and prevented the hydrolysis associated with nitrobenzoate and nitrophenylcarbamate linkages. As a result, the enantioseparations of nine triazole pesticides were achieved using NCDSP. Meanwhile, the chromatographic conditions, such as the pH and the composition of mobile phases, were investigated in detail. Moreover, in a comparative study with a cyclodextrin stationary phase (CDSP), the NCDSP provided higher enantioselectivity. Baseline separations for most of these triazoles on NDCSP were observed in relatively short times from 10 to 20 min. The highest resolution achieved was 2.87. Otherwise, incomplete enantiomeric separation was observed on the CDSP with a maximum resolution of less than 1.18. For the NCDSP, in addition to the inclusion effect, the π-π interaction between the electron-deficient stationary phase and the electron-donating triazoles significantly contributed to the chiral separation. This work reports a simple and convenient method for the preparation of the NCDSP with the rapid separation of chiral triazole pesticides.

High resolution HPLC-MS confirms overestimation of urea in soil by the diacetyl monoxime (DAM) colorimetric method

Urea represents a common form of organic nitrogen (N) which is added to agricultural soils in large quantities in both cropping (e.g. fertiliser) and livestock (e.g. urine) systems. In addition, there is a small, dynamic ambient pool of urea in soil associated with metabolic functioning in the microbial community. The diacetyl monoxime (DAM) colorimetric method is routinely used to quantify urea in soil, however, it lacks specificity due to the potential to react with the ureido group (R1NHCONHR2), a common structural moiety in soil organic matter. The aim of this study was therefore to critically evaluate the accuracy of this method for urea determination in soil. Using the DAM assay, we demonstrated significant cross-reactivity with a range of ureido compounds, many of which are ubiquitous in soil. We conclude therefore that the DAM assay is highly likely to overestimate urea concentrations in environmental materials. Such overestimation was confirmed using high resolution HPLC-Orbitrap MS to quantify urea in grassland soils using standard addition and the concentrations compared with those of the DAM assay. The results obtained show the DAM colorimetric method overestimated urea concentration by between 7.2 and 58 times for the sites studied. This significant overestimation of urea emphasises the need to validate the colorimetric method with reference to the LC-MS assay to ensure the robustness of measured urea concentrations. On this basis we recommend that reporting of the results from the DAM colorimetric method as “urea” concentration be curtailed and reported as “ureido-N” to recognise the contribution of unknown and variable contributions from other compounds. Indeed, given the problems with quantitatively assessing the latter contributions we would recommend the DAM method is now avoided in surveys of urea concentrations in soil and the wider environment.

Development of a highly sensitive fluorescence probe for peptidyl arginine deiminase (PAD) activity

Peptidyl arginine deiminases (PADs) catalyze the post-translational deimination of arginine residues to citrulline residues. Aberrant levels of PAD activity are associated with various diseases, such as rheumatoid arthritis, Alzheimer’s disease, and multiple sclerosis, so there is a need for simple and convenient high-throughput screening systems to discover PAD inhibitors as candidate therapeutic agents. Here, we report a highly sensitive off/on-type fluorescence probe for PAD activity based on the donor-excited photoinduced electron transfer (d-PeT) mechanism, utilizing the specific cycloaddition reaction between the benzil group of the probe and the ureido group of the PAD product, citrulline, under acidic conditions. We synthesized and functionally evaluated a series of probes bearing substituents on the benzil phenyl group, and found that 4MEBz-FluME could successfully detect citrulline with higher sensitivity and broader dynamic range than our previously reported fluorescence probe, FGME. Moreover, we succeeded in establishing multiple assay systems for PAD subtypes activities, including PAD2 and PAD4, with 4MeBz-FluME thanks to its high sensitivity. We expect that our fluorescence probes will become a powerful tool for discovering PAD inhibitors of several subtypes. Thus, it should be suitable for high-throughput screening of chemical libraries for inhibitors of PADs.

Steric Course of Deprotonation/Substitution of Chelating/Dipole‐Stabilizing‐Group‐Substituted α‐Amino‐ and α‐Oxynitriles

The stereochemical course of electrophilic substitutions of α‐nitrile metallocarbanions was investigated through the deprotonation of enantioenriched α‐amino‐ and α‐oxynitriles bearing a carbamoyl or methoxycarbonyl group in the presence of an electrophile. The results suggested that the dipole‐stabilizing substituents not only affected the configurational stability and chemical reactivity of the α‐nitrile metallocarbanions but could also change the steric course of the electrophilic substitution (retention vs. inversion). Whereas the reaction of an α‐aminonitrile bearing a dimethylaminocarbonyl group on the nitrogen atom with lithium hexamethyldisilazane in the presence of PhCOCl resulted in the formation of a retention product (93:7), the reaction of an α‐aminonitrile bearing a methoxycarbonyl group was reversed in favor of the inversion product (37:63). Thus, the methoxycarbonylamino group increased the degree of planarization of the anionic center with maintenance of the planar chirality more than the ureido group, which led to preferential attack of the electrophile from the rear face.

Allantoin and hydantoin as new protein aggregation suppressors

Allantoin is widely used in pharmaceutical and cosmetic products, and is composed of a hydantoin ring and a ureido group. Recent reports showed that allantoin suppresses thermal aggregation of hen egg white lysozyme (LYZ). However, structural insight into the properties of allantoin on protein aggregation and whether allantoin controls the aggregation of other proteins under different stress conditions remain unclear. Here we studied the structural properties of allantoin in terms of its effects on protein aggregation by comparing allantoin with urea and hydantoin. Furthermore, we analyzed the effects of allantoin and its derivatives on the aggregation of LYZ, carbonic anhydrase from bovine erythrocytes (BCA), albumin from chicken egg white (OVA), and immunoglobulin G (IgG) by various stresses in comparison with arginine. These four proteins are widely different in charged state and molecular size. Allantoin suppressed the aggregation and inactivation of LYZ comparing to arginine without affecting the melting temperature of proteins, and was responsible for the slightly improved formation of soluble oligomers and insoluble aggregates of IgG with thermal and acidic stresses. In contrast, hydantoin increased the solubility of aromatic amino acids more effectively than arginine and allantoin. The structural properties underlying the observed effects of allantoin as an aggregation suppressor include hydrophobic interactions between hydantoin moiety and aromatic ring on the surface of proteins, which is reflected on the difference between allantoin and arginine. These results show that the backbone of hydantoin ring may be a new category of additives for development of small aggregation suppressors.

Exploiting charge differences for the analysis of challenging post-translational modifications by capillary electrophoresis-mass spectrometry

Reversed-phase high-performance liquid chromatography (RP-HPLC) in combination with mass spectrometry (MS) is typically employed for mapping modifications in proteins and peptides. Here we applied a low-flow capillary electrophoresis (CE) −electrospray ionization interface coupled to Orbitrap mass spectrometers to analyze challenging modifications such as asparagine deamidation, aspartate isomerization, arginine citrullination, and phosphopeptide isomers. We achieved excellent resolution of asparagine (Asn), aspartic acid (Asp) and isoaspartic acid (iso-Asp) containing peptides using a synthetic peptide mixture. The migration order in CE enabled a clear assignment of in vitro deamidation/isomerization sites in a protein standard mixture of intermediate complexity (48 proteins) as well as the determination of the in vivo deamidation rate of histone H1.0 directly in a crude nuclear protein fraction. Besides these well-known modifications citrullination, a post-translational modification which changes the positively charged guanidinium group of arginine to the uncharged ureido group of citrulline, was investigated. Applying CE-MS for fast and sensitive analyses of various post-translational modifications of intact and enzymatically digested histone H4, we were able to detect a variety of citrullinated proteoforms. MS/MS analysis with electron transfer dissociation (ETD) fragmentation identified the presence of deiminated Arg at position 3 and 17 of histone H4. Moreover, based on CE-MS, isobaric mono-phosphorylated peptides obtained in the course of a kinase activity study were separated and individual positional isomers quantified.

Human Deiminases: Isoforms, Substrate Specificities, Kinetics, and Detection.

Peptidylarginine deiminase (PAD) enzymes are of enormous interest in biomedicine. They catalyze the conversion of a positively-charged guanidinium at an arginine side chain into a neutral ureido group. As a result of this conversion, proteins acquire the non-ribosomally encoded amino acid "citrulline". This imposes critical influences on the structure and function of the target molecules. In multiple sclerosis, myelin hyper-citrullination promotes demyelination by reducing its compaction and triggers auto-antibody production. Immune responses to citrulline-containing proteins play a central role in the pathogenesis of autoimmune diseases. Moreover, auto-antibodies, specific to citrullinated proteins, such as collagen type I and II and filaggrin, are early detectable in rheumatoid arthritis, serving as diagnostic markers of the disease. Despite their significance, little is understood about the role in demyelinating disorders, diversified cancers, and auto-immune diseases. To impart their biological and pathological effects, it is crucial to better understand the reaction mechanism, kinetic properties, substrate selection, and specificities of peptidylarginine deiminase isoforms.Many aspects of PAD biochemistry and physiology have been ignored in past, but, herein is presented a comprehensive survey to improve our current understandings of the underlying mechanism and regulation of PAD enzymes.