An OFF-ON fluorescent probe for Zn2+ based on a GFP-inspired imidazolone derivative attached to a 1,10-phenanthroline moiety

A green fluorescent protein chromophore inspired chemosenor for Zn(2+) was designed and synthesized. A Zn(2+) specific fluorescence enhancement was observed due to restricted rotation between the 1,10-phenanthroline and imidazolone moieties.     

Color Tuning of Fluorogens for FAST Fluorogen-Activating Protein

Using benzylidene imidazolone core, we created a panel of color-shifted fluorogenic ligands for FAST protein without compromise to the binding efficiency and the utility for live-cell protein labeling. This study highlights the potential of benzylidene imidazolones derivatives for rapid expansion of a pallet of live-cell fluorogenic labeling tools.     

A Multicolor Large Stokes Shift Fluorogen-Activating RNA Aptamer with Cationic Chromophores

Large Stokes shift (LSS) fluorescent proteins (FPs) exploit excited state proton transfer pathways to enable fluorescence emission from the phenolate intermediate of their internal 4-hydroxybenzylidene imidazolone (HBI) chromophore. An RNA aptamer named Chili mimics LSS FPs by inducing highly Stokes-shifted emission from several new green and red HBI analogues that are non-fluorescent when free in solution. The ligands are bound by the RNA in their protonated phenol form and feature a cationic aromatic side chain for increased RNA affinity and reduced magnesium dependence. In combination with oxidative functionalization at the C2 position of the imidazolone, this strategy yielded DMHBO⁺, which binds to the Chili aptamer with a low-nanomolar K_D. Because of its highly red-shifted fluorescence emission at 592 nm, the Chili–DMHBO⁺ complex is an ideal fluorescence donor for Förster resonance energy transfer (FRET) to the rhodamine dye Atto 590 and will therefore find applications in FRET-based analytical RNA systems.     

Palladium-catalyzed direct arylation of imidazolone N-oxides with aryl bromides and its application in the synthesis of GSK2137305

The palladium-catalyzed direct arylation of imidazolone N-oxides with aryl bromides to afford the corresponding 4-aryl imidazolone N-oxides is described. This method has been successfully used for the synthesis of GSK2137305.     

Unusual oxidation behaviour of a propargylic alcohol

Attempts to convert a propargylic alcohol bearing an imidazolone substituent to the corresponding aldehyde under Parikh-Doering conditions gave an α,β-unsaturated-β-methylsulfanyl aldehyde, which cyclised under mildly acidic conditions.     

Pd(0)‐Catalyzed Direct C−H Functionalization of 2‐H‐4‐Benzylidene Imidazolones: Friendly and Large‐Scale Access to GFP and Kaede Protein Fluorophores

The first one‐pot synthesis of N‐substituted 2‐H‐4‐benzylidene imidazolones and their subsequent palladium‐catalyzed and copper‐assisted direct C2?H arylation and alkenylation with aryl‐ and alkenylhalides are described. This innovative synthesis is step‐economical, azide‐free, high yielding, highly flexible in the introduction of a variety of electronically different groups, and can be operated on large‐scale. Moreover, the method allows direct access to C2‐arylated or alkenylated imidazolone‐based green fluorescent protein (GFP) and Kaede protein fluorophores, including ortho‐hydroxylated models.     

Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein

Green fluorescent protein (GFP) was ionized by native electrospray ionization and trapped for many seconds in high vacuum, allowing fluorescence emission to be measured as a probe of its biological function, to answer the question whether GFP exists in the native form in the gas phase or not. Although a narrow charge‐state distribution, a collision cross‐section very close to that expected for correctly folded GFP, and a large stability against dissociation all support a near‐native gas‐phase structure, no fluorescence emission was observed. The loss of the native form is attributed to the absence of residual water in the gas phase, which normally stabilizes the para‐hydroxybenzylidene imidazolone chromophore of GFP.     

Synthesis of marine alkaloids leucettamines B and C by β-lactam ring rearrangement

A new method for the synthesis of marine alkaloids leucettamines B and C from Leucetta sp. sponges is described. The key step is the base-promoted rearrangement of β-lactam into imidazolone ring. Leucettamines B and C as well as their N-benzoyl derivatives were obtained in high yields. Single-crystal structures of both leucettamines B and C were determined by X-ray diffraction confirming Z-configuration of double bond at 4-position of imidazolone.     

Reaction of 2‐Phenyl‐4‐arylidene‐1,3‐oxazolones with Different Nucleophiles for Synthesis of Some New Heterocycles

Refluxing of 1,3‐oxazolone ( 1a ) with malononitrile in dry benzene and in the presence of ammonium acetate afforded imidazolone derivative ( 2 ). However, carrying out the same reaction in absolute ethanol and in the presence of piperidine as a base gave the benzamide derivative ( 4 ). Fusion of ( 1a ) with p‐anisidine gave the open adduct benzamide ( 6 ), which cyclized in acidic medium to give imidazolone derivative ( 7 ). Heating of imidazolone ( 7 ) with malononitrile above its melting point afforded 1,3‐diazepine derivative ( 8 ). Reaction of the carbohydrazide ( 9 ) with isatin in ethanol gives the corresponding Schiff base ( 11 ), which then reacted with acetyl acetone, ethyl acetoacetate, ethyl cyanoacetate, and malononitrile in n‐butanol and piperidine to afford benzamide derivative ( 13 , 14 , 15 ) and ( 16 ), respectively. The structures of the newly synthesized compounds were established on the basis of IR, ¹H‐NMR, mass spectra, and elemental analyses.     

Development of chiral pincer palladium complexes bearing a pyrroloimidazolone unit. Catalytic use for asymmetric Michael addition

Novel pincer palladium complexes having chiral hexahydro-1H-pyrrolo[1,2-c]imidazolone groups were designed and prepared. Catalytic asymmetric Michael addition of isopropyl 2-cyanopropionate to ethyl vinyl ketone was catalyzed by the chiral pincer palladium complex to give isopropyl 2-cyano-2-methyl-5-oxoheptanoate with high enantioselectivity (up to 83% ee). [structure: see text]     

Oxidation of guanine bases mediated by a manganese-porphyrin-oligonucleotide conjugate onto a G-rich DNA target: 8-oxo-7,8-dihydroguanine is not the major lesion

The oxidative alkali-labile G lesions mediated by manganese porphyrin oligonucleotide conjugate on a DNA target could not be attibuted to the formation of 8-oxo-7,8-dihydroguanine since they were not substrate of the Fpg protein. In order to identify the nature of these lesions, an analysis of the oxidized derivatives of 2′-deoxyguanosine, imidazolone and oxazolone, generated by photooxidation, was efficiently performed by using the positive electrospray ionisation-mass spectrometry method.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

New ditopic organic ligands with 2-pyridylbenzothiazole and 5-pyridylmethylidene-2-(methylthio)imidazolone fragments

Russian Chemical Bulletin - New ditopic organic ligands with (pyridylmethylidene)imidazolone and pyridylbenzothi-azole moieties were synthesized by Cu-catalyzed azide-alkyne cycloaddition of...     

A single point mutation converts a proton-pumping rhodopsin into a red-shifted,turn-on fluorescent sensor for chloride

The visualization of chloride in living cells with fluorescent sensors is linked to our ability to design hosts that can overcome the energetic penalty of desolvation to bind chloride in water. Fluorescent proteins can be used as biological supramolecular hosts to address this fundamental challenge. Here, we showcase the power of protein engineering to convert the fluorescent proton-pumping rhodopsin GR from Gloeobacter violaceus into GR1, a red-shifted, turn-on fluorescent sensor for chloride in detergent micelles and in live Escherichia coli. This non-natural function was unlocked by mutating D121, which serves as the counterion to the protonated retinylidene Schiff base chromophore. Substitution from aspartate to valine at this position (D121V) creates a binding site for chloride. The binding of chloride tunes the pK_a of the chromophore towards the protonated, fluorescent state to generate a pH-dependent response. Moreover, ion pumping assays combined with bulk fluorescence and single-cell fluorescence microscopy experiments with E. coli, expressing a GR1 fusion with a cyan fluorescent protein, show that GR1 does not pump ions nor sense membrane potential but instead provides a reversible, ratiometric readout of changes in extracellular chloride at the membrane. This discovery sets the stage to use natural and laboratory-guided evolution to build a family of rhodopsin-based fluorescent chloride sensors with improved properties for cellular applications and learn how proteins can evolve and adapt to bind anions in water.

By utilizing laboratory-guided evolution, we have converted the fluorescent proton-pumping rhodopsin GR from Gloeobacter violaceus into GR1, a red-shifted, turn-on fluorescent sensor for chloride.     

Sequential [3+2] cycloaddition/rearrangement reaction of imidazolone nitrones and allenoates for the efficient synthesis of functionalized imidazolidinone

Sequential [3+2] cycloaddition/rearrangement reaction of imidazolone nitrones and allenoates is described. The reaction was carried out in refluxing toluene to provide the methylene imidazolidinone derivatives in high yield. It provides a simple and convenient strategy for the synthesis of functionalized imidazolidinones.     

Photooxidation of 2'-deoxyguanosine 5'-monophosphate in aqueous solutions

Mass spectrometric and ultraviolet absorption spectral evidence are presented for the assignment of structures to three products detected in the reaction mixtures formed upon the photolysis of aqueous solutions of the nucleotide 2'-deoxyguanosine 5'-monophosphate (dGMP) with light of wavelengths >270 nm. The products for which structures are assigned are spiroiminodihydantoin 2'-deoxyribonucleotide (1), 2,2-diamino-4-([2-deoxy-5-monophosphate-beta-D-erythro-pentofuranosyl]amino)-5-(2H)-oxazolone (oxazolone 2'-deoxyribonucleotide, 2) and 2-amino-5-([2-deoxy-5-monophosphate-beta-D-erythro-pentofuranosyl]amino)-4H-imidazol-4-one (imidazolone 2'-deoxyribonucleotide, 3). These results, when combined with mechanistic data presented in an earlier communication, provide support for the proposal that the irradiation of dGMP with UVB light leads to the formation of singlet oxygen. The UV absorption spectral properties of the imidazolone make this product a reasonable candidate to rationalize the autosensitization of dGMP degradation reported in the earlier communication.     

Discovery and mutagenicity of a guanidinoformimine lesion as a new intermediate of the oxidative deoxyguanosine degradation pathway

Oxidative degradation of DNA is a major mutagenic process. Reactive oxygen species (ROS) produced in the course of oxidative phosphorylation or by exogenous factors are known to attack preferentially deoxyguanosine. The latter decomposes to give mutagenic lesions, which under physiological conditions are efficiently repaired by specialized maintenance systems in the cell. Although many intermediates of the degradation pathway are today well-known, we report in this study the discovery of a new intermediate with an interesting guanidinoformimine structure. The structure elucidation of the new lesion was possible by using HPLC-MS techniques and organic synthesis. Finally we report the mutagenic potential of the new lesion in comparison to the known lesions imidazolone and oxazolone using primer extension and pyrosequencing experiments.     

Synthesis and properties of aroyl derivatives of 2-imidazolone and 2-benzimidazolone

A series of C-aroyl derivatives of 2-imidazolone and 2-benzimidazolone has been obtained by the reaction of the chlorides of the corresponding carboxylic acids with imidazolone and benzimidazolone in the presence of anhydrous aluminum chloride. A consideration of the IR spectra has shown that the substances synthesized have the lactam structure in the solid state.     

Lithiation and Electrophilic Substitution of Dimethyl Triazones

The lithiation and electrophilic substitution of dimethyl triazones is described. Directed lithiation or tin-lithium exchange of dimethyl triazones afforded the corresponding dipole stabilized nucleophiles that were trapped with various electrophiles. Keto-triazone derivatives accessed by acylation of such nucleophiles were readily converted into the corresponding imidazolone heterocycles.