Reaction of Nitric Oxide with Amines

Development of a urea-bond cleavage reaction induced by nitric oxide for fluorescence imaging

Nitric oxide (NO) is a multifunctional signalling molecule with indispensable roles in physiological processes, but its abnormal production is implicated in various disease conditions. Detecting NO is crucial for interrogating its biological roles. Although many o-phenylenediamine-based fluorescent probes have been developed, only a small fraction has been employed in vivo. Moreover, these probes largely require direct modifications of the fluorophore backbones to render NO responsiveness, which restricts the general applicability of o-phenylenediamine-based probe designs to other types of fluorophores. Here, we report the rational development, optimization, and application of a NO-induced urea-bond cleavage reaction for selective fluorescence detection and imaging of NO in living systems. Through rational design and extensive screening, we identified a 2-aminophenylurea-derived functionality that can react with NO through N-nitrosation, acyltriazole formation, and hydrolysis to induce the cleavage of the urea bond and release of the amino-containing coumarin fluorophore. By caging different amino-containing fluorophore scaffolds with the 2-aminophenylurea-derived functionality, we modularly developed a series of NO fluorescent probes with different excitation and emission profiles for the detection of NO in aqueous solutions and live cells. Among these probes, the near-infrared probe has been demonstrated to enable in vivo fluorescence visualization of elevated endogenous levels of NO in a murine inflammation model. Overall, this study provides a NO-induced urea-bond cleavage reaction and establishes the utility of this reaction for the general and modular development of NO fluorescent probes, thus opening new opportunities for studying and manipulating NO in biological systems.

Quantification of Nitric Oxide in Single Cells Using the Single-Probe Mass Spectrometry Technique

Nitric oxide (NO) is a small molecule that plays important roles in biological systems and human diseases. The abundance of intracellular NO is tightly related to numerous biological processes. Due to cell heterogeneity, the intracellular NO amounts significantly vary from cell to cell, and therefore, any meaningful studies need to be conducted at the single-cell level. However, measuring NO in single cells is very challenging, primarily due to the extremely small size of single cells and reactive nature of NO. In the current studies, the quantitative reaction between NO and amlodipine, a compound containing the Hantzsch ester group, was performed in live cells. The product dehydro amlodipine was then detected by the Single-probe single-cell mass spectrometry technique to quantify NO in single cells. The experimental results indicated heterogeneous distributions of intracellular NO amounts in single cells with the existence of subpopulations.

A MOF Multifunctional Cargo Vehicle for Reactive Gas Delivery and Catalysis

Efficient delivery of reactive and toxic gaseous reagents to organic reactions was studied using metal-organic frameworks (MOFs). Simultaneous cargo vehicle and catalytic capabilities of several MOFs were probed for the first time using the examples of  aromatization, aminocarbonylation, and carbonylative Suzuki-Miyaura coupling reactions. These reactions highlight that MOFs can serve a dual role as a gas cargo vehicle and a catalyst,  leading to product formation with yields similar to reactions employing pure gases. Furthermore, the MOFs can be recycled without sacrificing product yield, while simultaneously maintaining crystallinity. The reported findings were supported crystallographically and spectroscopically (e.g.,  diffuse reflectance infrared Fourier transform spectroscopy), foreshadowing a pathway for the development of multifunctional MOF-based reagent-catalyst cargo vessels for reactive reagents, as an attractive alternative to the use of toxic pure gases or gas generators.

Measurement of Intracellular Nitric Oxide with a Quantitative Mass Spectrometry Probe Approach

Nitric oxide (NO) is a molecule of physiological importance, and the function of NO depends on its concentration in biological systems, particularly in cells. Concentration-based analysis of intracellular NO can provide insight into its precise role in health and disease. However, current methods for detecting intracellular NO are still inadequate for quantitative analysis. In this study, we report a quantitative mass spectrometry probe approach to measure NO levels in cells. The probe, Amlodipine (AML), comprises a Hantzsch ester group that reacts with NO to form a pyridine, Dehydro Amlodipine (DAM). Quantification of DAM by ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) allows specific measurement of intracellular NO levels. Notably, the AML/NO reaction proceeds rapidly (within 1 s), which is favorable for NO detection considering its large diffusivity and short half-life. Meanwhile, studies under simulated physiological conditions revealed that the AML response to NO is proportional and selective. The presented UPLC-MS/MS method showed high sensitivity (LLOQ = 0.24 nM) and low matrix interference (less than 15%) in DAM quantification. Furthermore, the mass spectrometry probe approach was demonstrated by enabling the measurement of endogenous and exogenous NO in cells. Hence, the quantitative UPLC-MS/MS method developed using AML as a probe is expected to be a new method for intracellular NO analysis.

Recent progress on the organic and metal complex-based fluorescent probes for monitoring nitric oxide in living biological systems

Nitric oxide (NO) is an important gaseous signaling molecule related to various human diseases. To investigate the biological functions of NO, many strategies have been developed for real-time monitoring the NO levels in biological systems. Among these strategies, fluorescent probes are considered to be one of the most efficient and applicable methods owing to their excellent sensitivity and selectivity, high spatiotemporal resolution, noninvasiveness, and experimental convenience. Therefore, great efforts have been paid to the design, synthesis, and fluorescence investigation of novel NO fluorescent probes in the past several years. However, few of them exhibit practical applications owing to the low concentration, short half-life, and rapid diffusion characteristics of NO in biological systems. Rational design of NO fluorescent probes with excellent selectivity and sensitivity, low cytotoxicity, long-lived fluorescent emission, and low background interference is still a challenge for scientists all over the word. To provide spatial-temporal information, this article focuses on the progress made in the organic and metal complex-based NO fluorescent probes during the past five years. The key structural elements and sensing mechanisms of NO fluorescent probes are discussed. Some novel ratiometric, luminescence, and photoacoustic probes with low background interference and deep tissue penetrating ability are mentioned. All these probes have been used for imaging exogenous and endogenous NO in cells and animal models. More importantly, this article also describes the development of multi-functional NO fluorescent probes, such as organelle targeting probes, dual-analysis probes, and probe-drug conjugates, which will inspire the design of various functional fluorescent probes.

RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

Background

The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical in a chassis organism is computationally intractable. Many current methods provide a single solution to this problem, but fail to provide all optimal pathways, optional sub-optimal solutions or hybrid biological/non-biological solutions.

Results

Here we present RetSynth, software with a novel algorithm for determining all optimal biological pathways given a starting biological chassis and target chemical. By dynamically selecting constraints, the number of potential pathways scales by the number of fully independent pathways and not by the number of overall reactions or size of the metabolic network. This feature allows all optimal pathways to be determined for a large number of chemicals and for a large corpus of potential chassis organisms. Additionally, this software contains other features including the ability to collect data from metabolic repositories, perform flux balance analysis, and to view optimal pathways identified by our algorithm using a built-in visualization module. This software also identifies sub-optimal pathways and allows incorporation of non-biological chemical reactions, which may be performed after metabolic production of precursor molecules.

Conclusions

The novel algorithm designed for RetSynth streamlines an arduous and complex process in metabolic engineering. Our stand-alone software allows the identification of candidate optimal and additional sub-optimal pathways, and provides the user with necessary ranking criteria such as target yield to decide which route to select for target production. Furthermore, the ability to incorporate non-biological reactions into the final steps allows determination of pathways to production for targets that cannot be solely produced biologically. With this comprehensive suite of features RetSynth exceeds any open-source software or webservice currently available for identifying optimal pathways for target production.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-3025-9) contains supplementary material, which is available to authorized users.

VUV-photolysis of aqueous solutions of hydroxylamine and nitric oxide. Effect of organic matter: phenol

VUV-irradiation of aqueous solutions containing hydroxylamine (NH₂OH) in its acid form (NH₃OH⁺) and phenol (C₆H₅OH) results in the simultaneous mineralization of the organic substrate and the almost quantitative reduction of NH₃OH⁺ to ammonium ions (NH₄⁺). Irradiation of aqueous solutions of NH₃OH⁺ in the absence of organic substrates showed the formation of nitrate (NO₃^-) and nitrite (NO₂^-) and minor quantities of NH₄⁺. In line with these experiments, VUV-irradiation of aqueous solutions of nitrogen monoxide (NO˙) yields NH₄⁺ only when C₆H₅OH is simultaneously mineralized. A possible reaction mechanism is discussed, where reactions of NO˙ and NH₃OH⁺ with hydrogen atoms (H˙), hydroxyl radicals (HO˙) and hydrated electrons (e^-_aq), all generated by the VUV-photochemically initiated homolysis of water, are of great importance to the observed results. In the presence of phenol, competition between phenol and either NO˙ or NH₃OH⁺ for these reactive intermediates in the primary volume of reactions strongly determines the oxidation state and nature of the N-containing products. C-Centered radicals and intermediate products of reactions may also have an important effect on the overall mechanism. The present results are discussed in relation to the actual state of knowledge presented in the literature.

An Efficient Method for the Oxidation of 1,4-Dihydropyridines under Mild and Heterogeneous Conditions via in Situ Generation of NOCl

A combination of inorganic chloride salts [e.g. AlCl3, ZrCl4, and ZnCl2] and sodium nitrite in the presence of wet SiO2 was used as an effective oxidising agent for the oxidation of dihydropyridines to their corresponding pyridine derivatives under mild and heterogeneous conditions in moderate to excellent yields.

Reactions of Propargylic Alcohols with Nitric Oxide

Propargylic alcohols are selectively oxidised by nitric oxide and trace oxygen to the corresponding carbonyl compounds (ynones) at ambient temperature in acetonitrile.

Tl(NO3)3. 3H2O: A Convenient Oxidising Agent for aromatisation of Hantzsch 1,4-dihydropyridines

An efficient oxidative aromatisation of Hantzsch 1,4-dihydropyridines to the corresponding pyridines by using Tl(NO3)3. 3H2O at ambient temperature is reported. The reactions were fast and the products were isolated in high yields.

An Efficient and Chemoselective Method for the Oxidation of 1,4-dihydropyridines under mild and heterogeneous conditions

A combination of inorganic acidic salts or oxalic acid dihydrate and sodium nitrate in the presence of wet SiO2 was used as an effective oxidising agent for the oxidation of dihydropyridines to their corresponding pyridine derivatives at 40–50 oC with excellent yields.

Nitric Oxide Analyzer Quantification of Plant S-Nitrosothiols

Nitric oxide (NO) is a small diatomic molecule that regulates multiple physiological processes in animals, plants, and microorganisms. In animals, it is involved in vasodilation and neurotransmission and is present in exhaled breath. In plants, it regulates both plant immune function and numerous developmental programs. The high reactivity and short half-life of NO and cross-reactivity of its various derivatives make its quantification difficult. Different methods based on calorimetric, fluorometric, and chemiluminescent detection of NO and its derivatives are available, but all of them have significant limitations. Here we describe a method for the chemiluminescence-based quantification of NO using ozone-chemiluminescence technology in plants. This approach provides a sensitive, robust, and flexible approach for determining the levels of NO and its signaling products, protein S-nitrosothiols.

Oxidative dehydrogenation of C-C and C-N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

Nitrogen heteroarenes form an important class of compounds which can be found in natural products, synthetic drugs, building blocks etc. Among the diverse strategies that were developed for the synthesis of nitrogen heterocycles, oxidative dehydrogenation is extremely effective. This review discusses various oxidative dehydrogenation strategies of C-C and C-N bonds to generate nitrogen heteroarenes from their corresponding heterocyclic substrates. The strategies are categorized under stoichiometric and catalytic usage of reagents that facilitate such transformations. The application of these strategies in the synthesis of nitrogen heteroarene natural products and synthetic drug intermediates are also discussed. We hope this review will arouse sufficient interest among the scientific community to further advance the application of oxidative dehydrogenation in the synthesis of nitrogen heteroarenes.

4-nitroso-sulfamethoxazole generation in soil under denitrifying conditions: Field observations versus laboratory results

The formation of 4-nitroso-sulfamethoxazole and 4-nitro-SMX, two transformation products (TPs) of sulfamethoxazole (SMX) was investigated under batch soil slurry experiments and in a field study. Due to their low occurrence levels (ng/L) in environmental waters, a suitable analytical method based on liquid chromatography - high resolution - mass spectrometry was developed. Consequently, field observations revealed, for the first time, the occurrence of 4-nitroso-SMX in groundwater at concentrations as high as 18ng/L.Nitric oxide (NO) steady-state concentrations were determined in soil slurry experiments because this reactive specie accounted for the formation of 4-nitroso-SMX and 4-nitro-SMX. Measurements revealed that environmental SMX concentrations (0.2-2μg/L) at neutral pH induced the accumulation of nitric oxide. Under acidic conditions (pH<6), nitrous acid (HONO) was the major source of nitric oxide while under neutral/basic conditions nitric oxide release was related to the inhibition of denitrification processes. Under laboratory experiments, SMX nitration reaction appeared to be an irreversible transformation pathway, while 4-nitroso-SMX was slowly transformed over time. The occurrence of 4-nitroso-SMX conditions was therefore unexpected in the field study but could be due to its continuous input from soil and/or its relative persistence under anoxic conditions. A mechanism for 4-nitroso-SMX formation was proposed involving a nitrosative desamination pathway through a phenyl radical.

Highly specific C-C bond cleavage induced FRET fluorescence for in vivo biological nitric oxide imaging

A novel Förster resonance energy transfer (FRET) fluorescence "off-on" system based on the highly specific, sensitive and effective C-C bond cleavage of certain dihydropyridine derivatives was reported for real-time quantitative imaging of nitric oxide (NO). 1,4-Dihydropyridine was synthesized as a novel linker which could connect customized fluorophores and their corresponding quenchers. The specific and quantitative response to NO is confirmed using fluorescence spectrometry with the classical example of fluorescein isothiocyanate (FITC) and [4'-(N,N'-dimethylamino)phenylazo] benzoyl (DABCYL). The fluorescence intensity increased linearly with the increase in the amount of NO. Cells incubated with an exogenous NO donor emitted fluorescence as expected. A high fluorescence intensity was detected in macrophages which generate NO when incubated with lipopolysaccharide (LPS). The in vivo imaging shows about an 8-fold contrast between Freund's adjuvant stimulated feet and normal feet in mice after intravenous injection, which was the first example of in vivo semiquantitative fluorescence imaging of NO in mammals.

Methods for the detection and determination of nitrite and nitrate: A review

Various techniques for the determination of nitrite and/or nitrate developed during the past 15 years were reviewed in this article. 169 references were covered. The detection principles and analytical parameters such as matrix, detection limits and detection range of each method were tabulated. The advantages and disadvantages of various methods were evaluated. In comparison to other methods, spectrofluorimetric methods have become more attractive due to its facility availability, high sensitivity and selectivity, low limits of detection and low-cost.

Aromatic primary monoamine-based fast-response and highly specific fluorescent probes for imaging the biological signaling molecule nitric oxide in living cells and organisms

Two fast-response and highly specific NO fluorescent probes were developed, based on the reductive deamination reaction of p-methoxyaniline with NO in aerobic conditions.

Water-soluble Hantzsch ester as switch-on fluorescent probe for efficiently detecting nitric oxide

A water soluble Hantzsch ester derivative of coumarin, DHPS, was synthesized and successfully applied in the fluorescent sensing nitric oxide (NO) in aqueous solution. The fluorescence of probe DHPS is extremely weak, while its fluorescence was greatly switched on upon the addition of NO solution and showed high selectivity and sensitivity to NO. The limitation of the detection was calculated to be 18nM. The NO-induced aromatization of dihydropyridine in DHPS to pyridine derivative (PYS) proved to be the switching mechanism for the fluorescent sensing process, which was confirmed through spectra characterization and computation study. Cytotoxicity assay demonstrated both DHPS and PYS are biocompatible, the DHPS was successfully applied to track the endogenously produced NO in the RAW 264.7 cells.

Biotic nitrosation of diclofenac in a soil aquifer system (Katari watershed, Bolivia)

Up till now, the diclofenac (DCF) transformation into its nitrogen-derivatives, N-nitroso-DCF (NO-DCF) and 5-nitro-DCF (NO2-DCF), has been mainly investigated in wastewater treatment plant under nitrification or denitrification processes. This work reports, for the first time, an additional DCF microbial mediated nitrosation pathway of DCF in soil under strictly anoxic conditions probably involving codenitrification processes and fungal activities. This transformation pathway was investigated by using field observations data at a soil aquifer system (Katari watershed, Bolivia) and by carrying out soil slurry batch experiments. It was also observed for diphenylamine (DPA). Field measurements revealed the occurrence of NO-DCF, NO2-DCF and NO-DPA in groundwater samples at concentration levels in the 6-68s/L range. These concentration levels are more significant than those previously reported in wastewater treatment plant effluents taking into account dilution processes in soil. Interestingly, the p-benzoquinone imine of 5-OH-DCF was also found to be rather stable in surface water. In laboratory batch experiments under strictly anoxic conditions, the transformation of DCF and DPA into their corresponding N-nitroso derivatives was well correlated to denitrification processes. It was also observed that NO-DCF evolved into NO2-DCF while NO-DPA was stable. In vitro experiments showed that the Fisher-Hepp rearrangement could not account for NO2-DCF formation. One possible mechanism might be that NO-DCF underwent spontaneous NO loss to give the resulting intermediates diphenylaminyl radical or nitrenium cation which might evolve into NO2-DCF in presence of NO2 radical or nitrite ion, respectively.

Highly sensitive ratiometric fluorescence probes for nitric oxide based on dihydropyridine and potentially useful in bioimaging

Hantzsch dihydropyridine-based ratiometric fluorescent NO probes, viz.PyNO and TPANO, were synthesized and characterized.

Aqueous phase nitric oxide detection by an amine-decorated metal–organic framework

Selective and sensitive aqueous phase nitric oxide (NO) detection by ligand modulation in an amine-functionalized metal–organic framework has been demonstrated.

The rational design of a highly sensitive and selective fluorogenic probe for detecting nitric oxide

A small-molecule fluorogenic probe for nitric oxide (NO) detection based on a new switching mechanism is developedviaa rational design.

Nitric oxide promotes recycling of 8-nitro-cGMP, a cytoprotective mediator, into intact cGMP in cells

8-Nitro-cGMP is an endogenous nucleotide discovered under inflammation conditions as an important mediator of nitric oxide (NO) signaling. Besides cGMP-like behaviour, 8-nitro-cGMP exerts unique cytoprotective effects against oxidative stress. Although the formation of 8-nitro-cGMP from 8-nitro-GTP has previously been proposed, the mechanism by which excess or unused 8-nitro-cGMP is removed from cells remains unknown. In this study, we report a nitric oxide-dependent cellular conversion of 8-nitro-cGMP to intact cGMP in RAW 264.7 macrophage cells. In our experiments, we synthesized isotopically labeled 8-nitro-cGMP as a tool for metabolites analysis and identified 8-amino-cGMP as an initial metabolite of 8-nitro-cGMP using a LC-MS/MS technique. We also proved that endogenous 8-nitro-cGMP can be converted into 8-amino-cGMP by immunocytochemical staining with an antibody that specifically recognizes 8-amino-cGMP. Moreover, we showed that isotopically labeled 8-amino-cGMP is metabolized into cGMP under inflammation conditions. We propose that nitrosylation of 8-amino-cGMP occurs by NO formation under stress conditions and gives putative 8-diazonium-cGMP, which subsequently decomposes into cGMP. To the best of our knowledge, this study is the first to report reductive deamination of aminoguanine nucleotide at the C-8 position. The findings of this study collectively indicate that NO plays a crucial role not only in the production of 8-nitro-cGMP but also in its elimination under oxidative stress or inflammation.

Nitric oxide turn-on fluorescent probe based on deamination of aromatic primary monoamines

The stable, water-soluble, and nonfluorescent FA-OMe can sense nitric oxide (NO) and form the intensely fluorescent product dA-FA-OMe via reductive deamination of the aromatic primary amine. The reaction is accompanied by a notable increase of the fluorescent quantum yield from 1.5 to 88.8%. The deamination mechanism of FA-OMe with NO was proposed in this study. The turn-on fluorescence signals were performed by suppression of photoinduced electron transfer (PeT), which was demonstrated by density functional theory (DFT) calculations of the components forming FA-OMe and dA-FA-OMe. Furthermore, FA-OMe showed water solubility and good stability at physiological pHs. Moreover, the selectivity study indicated that FA-OMe had high specificity for NO over other reactive oxygen/nitrogen species. In an endogenously generated NO detection study, increasing the incubation time of FA-OMe with lipopolysaccharide (LPS) pretreated Raw 264.7 murine macrophages could cause an enhanced fluorescence intensity image. In addition, a diffusion/localization cell imaging study showed that FA-OMe could be trapped in Raw 264.7 cells. These cell imaging results demonstrated that FA-OMe could be used as a turn-on fluorescent sensor for the detection of endogenously generated NO.