Chemical Derivatization Research Articles

Mass Spectrometry-Based Precise Identification of Citrullinated Histones via Limited Digestion and Biotin Derivative Tag Enrichment.

Histone citrullination is an essential epigenetic post-translational modification (PTM) that affects many important physiological and pathological processes, but effective tools to study histone citrullination are greatly limited due to several challenges, including the small mass shift caused by this PTM and its low abundance in biological systems. Although previous studies have reported frequent occurrences of histone citrullination, these methods failed to provide a high-throughput and site-specific strategy to detect histone citrullination. Recently, we developed a biotin thiol tag that enabled precise identification of protein citrullination coupled with mass spectrometry. However, very few histone citrullination sites were identified, likely due to the highly basic nature of these proteins. In this study, we develop a novel method utilizing limited digestion and biotin derivative tag enrichment to facilitate direct in vivo identification of citrullination sites on histones. We achieve improved coverage of histone identification via partial enzymatic digestion and lysine block by dimethylation. With biotin tag-assisted chemical derivatization and enrichment, we also achieve precise annotation of histone citrullination sites with high confidence. We further compare different fragmentation methods and find that the electron-transfer-dissociation-based approach enables the most in-depth analysis and characterization. In total, we unambiguously identify 18 unique citrullination sites on histones in human astrocytoma U87 cells, including 15 citrullinated sites being detected for the first time. Some of these citrullination sites are observed to exhibit noticeable alterations in response to DNA damage, which demonstrates the superiority of our strategy in understanding the roles of histone citrullination in critical biological processes.

Okeanic acid–A, a trihydroxy fatty acid from the Okinawan cyanobacterium Okeania hirsuta

Trihydroxy fatty acids are oxidative metabolites of polyunsaturated fatty acids isolated from plants, bacteria, fungi, and microalgae and have a variety of biological activities. In this study, a new trihydroxy fatty acid, okeanic acid–A (1), was isolated together with malyngic acid (2) and 15,16-dihydromalyngic acid (3) from the cyanobacterium Okeania hirsuta collected in Okinawa, Japan. The planar structure of 1 was elucidated by detailed analyses using high-resolution ESI-MS and 1D and 2D NMR spectroscopy. The absolute configurations of the hydroxy groups in 1 were determined unambiguously by chemical derivatisation and a modified Mosher’s method. These cyanobacterial trihydroxy fatty acids (1–3) have identical configurations at their respective trihydroxy parts. Okeanic acid–A (1) showed mild growth-inhibitory activity against the marine diatom Nitzschia amabilis.

Inaoside A: New antioxidant phenolic compound from the edible mushroom Laetiporus cremeiporus

Laetiporus cremeiporus is the edible mushroom distributed in East Asia. It has been reported that an extract of L. cremeiporus exhibited DPPH radical scavenging activity. The aim of this study is to identify the antioxidant compound from L. cremeiporus. Guided by DPPH radical scavenging activity, a new antioxidant phenolic compound inaoside A (1) and three well-known bioactive compounds 5′-S-methyl-5′-thioadenosine (MTA, 2), nicotinamide (3), and adenosine (4) were isolated from L. cremeiporus. An antioxidant compound was isolated from L. cremeiporus for the first time. This is the first report of the isolation of 1, 2, and 4 from L. cremeiporus. The structures were determined by one- and two-dimensional NMR spectroscopic analysis and chemical derivatization. The antioxidant activities of extracts, fractions, and isolated compounds were evaluated by a DPPH radical scavenging assay. Compound 1 exhibited significant DPPH radical scavenging activity (80 % inhibition at 100 μg/mL, IC50 79.9 μM, trolox equivalent antioxidant capacity (TEAC) = 0.36).

Structural elucidation of derivatives of polyfunctional metabolites after methyl chloroformate derivatization by high-resolution mass spectrometry gas chromatography. Application to microbiota metabolites

Metabolomics has become an essential discipline in the study of microbiome, emerging gas chromatography coupled to mass spectrometry as the most mature, robust, and reproducible analytical technique. Silylation is the most widely used chemical derivatization strategy, although it has some limitations. In this regard, alkylation by alkyl chloroformate offers some advantages, such as a rapid reaction, milder conditions, better reproducibility, and the generation of more stable derivatives. However, commercial spectral libraries do not include many of the alkyl derivatives, mainly for polyfunctional metabolites, which can form multiple derivatives. That introduces a huge bias in untargeted metabolomics leading to common errors such as duplicates, unknowns, misidentifications, wrong assignations, and incomplete results from which non-reliable findings and conclusions will be retrieved. For this reason, the purpose of this study is to overcome these shortcomings and to expand the knowledge of metabolites in general and especially those closely related to the gut microbiota through the thorough study of the reactivity of the different functional groups in real matrix derivatized by methyl chloroformate, a common representative alkylation reagent. To this end, a systematic workflow has been developed based on exhaustive structural elucidation, along with computational simulation, and taking advantage of the high sensitivity and high-resolution gas chromatography-mass spectrometry. Several empirical rules have been established according to chemically different entities (free fatty acids, amino acids, polyols, sugars, amines, and polyfunctional groups, etc.) to predict the number of derivatives formed from a single metabolite, as well as their elution order and structure. In this work, some methyl chloroformate derivatives not previously reported as well as the mechanisms to explain them are given. Extremely important is the interconversion of E- and Z- geometric isomers of unsaturated dicarboxylic acids (case of fumaric-maleic and case of citraconic-mesaconic acids), or the formation of cycled derivatives for amino acids, as well as common metabolites, as in the case of serine and cysteine, and many others.

Ethanolysis of nitrogen mustards: A novel strategy for nitrogen mustard identification in environmental matrices by liquid chromatography-electrospray ionization-tandem mass spectrometry.

Nitrogen mustards (NMs) are blistering chemical warfare agents. The ability to detect NMs in environmental samples is very important for obtaining forensic evidence. The most common analytical techniques for NM detection are gas chromatography-mass spectrometry, which detects NMs in their intact form but is disadvantaged by high limits of detection (LODs), and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) of their hydrolysis products, which do not provide robust evidence to support NM use. We developed a novel approach to detect and identify NMs using LC/ESI-MS/MS after chemical derivatization. The method is based on ethoxide-promoted ethanolysis prior to analysis. The effects of reaction time, temperature, ethoxide concentration and chromatography behavior were studied and optimized. In the developed procedure, 0.1% (v/v) sodium ethoxide solution is added to the NMs in ethanol and agitated for 2h at 50°C, followed by LC/ESI-MS/MS, without any other pretreatment. The ethanolysis reaction efficiencies were evaluated in ethanolic extracts from soil, asphalt, and ethanol contaminated with 0.5% (v/v) diesel fortified with NMs at a five-point calibration curve. The calibration curves showed good linearity in the range of 0.05-1ng/mL, with an R2 value of 0.99, and were similar to those of LC/MS-grade ethanol, with almost no observable matrix effects. The derivatization products were stable at room temperature, with LODs of 10pg/mL, in all investigated extracts. Through this newly developed strategy, the derivatization of active NMs by ethanolysis was achieved for the first time, and these derivatization products can serve as specific indicators for the use and presence of NMs. The methodology can also verify trace levels of NM chemical warfare agents collected in war or terror scenarios in forensic investigations.

Testacosides A–D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis

Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A–D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A–D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum.Key points• The first report of metabolites produced by Microbacterium testaceum.• 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified.• Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.Graphical abstract

Antifungal profile against Candida auris clinical isolates of tyroscherin and its new analog produced by the deep-sea-derived fungal strain Scedosporium apiospermum FKJ-0499.

A new antifungal compound, named N-demethyltyroscherin (1), was discovered from the static fungal cultured material of Scedosporium apiospermum FKJ-0499 isolated from a deep-sea sediment sample together with a known compound, tyroscherin (2). The structure of 1 was elucidated as a new analog of 2 by MS and NMR analyses. The absolute configuration of 1 was determined by chemical derivatization. Both compounds showed potent in vitro antifungal activity against clinically isolated Candida auris strains, with MIC values ranging from 0.0625 to 4 µg ml-1.

Rapid Identification of Phenolics in Mixtures by Two‐Dimensional Tandem Mass Spectrometry with Microdroplet Accelerated Derivatization Reactions

AbstractComplex mixtures are typically analyzed by chromatographic separation followed by mass spectrometry. Two‐dimensional tandem mass spectrometry (2D MS/MS) may eliminate the need for separation and therefore significantly reduce analysis time while expanding the information space by recording the intensities of all fragment ions generated from all trapped precursor ions. Additional chemical specificity can be provided by using chemical derivatization. In this study phenolic compounds are identified after triazole click derivatization by the observation of two diagnostic features in the 2D MS/MS data domain, a mass shift of 175 Da on the precursor ion axis and a neutral loss (NL) of 119 Da. Additional NL transitions were highly correlated with particular substituents including carbonyl, ester, amino, and alkyl/phenyl groups. Substituent position information was also easily diagnosed. The derivatization reactions are accelerated in the charged electrosprayed microdroplets. Using this method, members of this single class of compounds can be identified within 1–2 minutes while structural information on the individual compounds is acquired simultaneously.

Identification and quantification of bipyridyl dicarboxylic acid isomers by ion mobility spectrometry

The identification of positional isomers is of interest because different isomers have different chemical or biological functions and applications. The analysis of positional isomers is sometimes challenging since they have similar chemical structures and properties. For example, the analysis of mass cannot identify different positional isomers because they have identical mass-to-charge ratios and show a single mass peak in mass spectrometry. In this study, an efficient and simple qualitative and quantitative analytical method for differentiating 2,2′-bipyridine-3,3′-dicarboxylic acid (3,3′-BDA), 2,2′-bipyridine-4,4′-dicarboxylic acid (4,4′-BDA), and 2,2′-bipyridine-5,5′-dicarboxylic acid (5,5′-BDA) was developed by using ion mobility spectrometry (IMS). The results revealed that the three BDA isomers formed non-covalent complexes with cyclodextrins (CDs) and Mg2+ ions in the gas phase: [β-CD+3,3′/4,4′/5,5′-BDA+Mg]2+ and [γ-CD+3,3′/4,4′/5,5′-BDA+Mg]2+, which were distinguished by measuring the mobility of the complexes because of their spatial conformational differences. The peak-to-peak resolution (Rp-p) values of the three isomers of [γ-CD+3,3′/4,4′/5,5′-BDA+Mg]2+ reached 2.983 and 2.892, respectively. The conformations of the ternary complexes simulated by the theoretical calculations revealed the different interactions and shapes of the stereoisomers, and the predicted results agreed with the experimental results. Simultaneously, further studies on the collisional dissociation of the ternary complexes revealed that the dissociation energies of the different complex ions varied were different owing to the diverse different conformations. Finally, the relative quantitative analysis of the different isomers in mixed samples was performed and satisfactory linearity results (R2 > 0.99) were obtained. Thus, an effective analytical method was proposed for the identification and quantification of BDA isomers without chemical derivatization, offering a promising approach for the identification of similar derivatives or positional isomers that could be applied in various fields including chemicals and pharmaceuticals.

Allostreptopyrroles A-E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384.

Five new β-alkylpyrrole derivatives, allostreptopyrroles A-E (1-5), were isolated from the culture broth of Allostreptomyces RD068384. Their structures were elucidated by 1D and 2D NMR spectroscopic analyses, HRESIMS, and chemical derivatization. The absolute configurations of compounds 2 and 3 were predicted by comparison of experimental and calculated specific rotation data. Compounds 1-5 are the first examples of natural pyrroles substituted by formyl and carboxyl functionalities. Compounds 1, 4, and 5 showed cytotoxicity against Kasumi-1 human acute myeloblastic leukemia cells with IC50 values of 103, 105, and 105 μM, respectively, which are less active than the anticancer agent cisplatin, with an IC50 value of 70 μM.

Rapid differentiation of xylazine metabolites using SLIM IM-MS.

Xylazine represents an increased threat to the recreational drug market. In this study, we present a rapid strategy for identifying xylazine and differentiating its common isomeric metabolites using Structures for Lossless Ion Manipulations (SLIM) ion mobility coupled to high-resolution/tandem mass spectrometry (IM-HRMS/MS). Chemical derivatization using dansyl chloride also assisted with separations and led to identification of resolvable reaction product atropisomers.

Structure and transport properties of self-assembled nanofiltration membranes based on sustainably derived materials

The development of functional polymers using sustainable resources is an increasingly important pursuit. Unsaturated fatty acids represent a potentially interesting class of renewable materials for this purpose. Their unsaturated carbon bonds permit crosslinking to form solid polymers. Additionally, their carboxylic acid functional groups provide for the display of specific surface chemistry within the resulting polymers, and also enable chemical derivatization. Here, we explore the fabrication of nanometer-scale size-selective membranes using conjugated linoleic acid derived monomers. Potassium salt conjugated linoleic acid surfactants (KCLA) self-assembled to form hexagonally packed cylinders (HI) in an aqueous medium containing glycerol. This structure provides a highly ordered medium with aqueous-continuous channels for nanofiltration. The HI mesophase was crosslinked with the addition of bifunctional comonomers and the ordered structure was retained with good fidelity in the resulting thin polymer films (< 400 nm thick). These film function effectively as nanofiltration membranes, with a size cut-off of approximately 1.2 nm for charged solutes, while maintaining a high permeance of ∼ 9 LMH/bar. This performance is on par with several commercial nanofiltration membranes and these materials are therefore of potential interest for advancing sustainability concerns in practical nanofiltration applications.

Development and application of a multi-sugar assay to assess intestinal permeability.

Aim: Bioanalytical assays to measure rhamnose, erythritol, lactulose and sucralose in human urine and plasma were developed to support an indomethacin challenge study for intestinal permeability assessment in healthy participants.Methods: The multi-sugar assays utilized 5-μl sample matrix and a simple chemical derivatization with acetic anhydride, followed by RPLC-MS/MS detection.Results: Rhamnose and erythritol quantification was established between 1.00-1,000μg/ml in urine and 250-250,000ng/ml in plasma. For lactulose and sucralose, dynamic ranges of 0.1-100μg/ml (urine) and 25-25,000ng/ml (plasma) were applied for biological measurements.Conclusion: This work helped overcome some of the common analytical challenges associated with the bioanalysis of mono- and disaccharides and achieved improved limits of quantification.

Identification and quantification of N6-methyladenosine by chemical derivatization coupled with 19F NMR spectroscopy.

N 6-Methyladenosine (6mA) is a well-known prokaryotic DNA modification that has been shown to play epigenetic roles in eukaryotic DNA. Accurate detection and quantification of 6mA are prerequisites for molecular understanding of the impact of 6mA modification on DNA. However, the existing methods have several problems, such as high false-positive rate, time-consuming and complex operating procedures. Chemical sensors for the selective detection of 6mA modification are rarely reported in the literature. Fluorinated phenylboronic acid combined with 19F NMR analysis is an effective method for determining DNA or RNA modification. In this study, we presented a simple and fast chemical method for labelling the 6th imino group of 6mA using a boric-acid-derived probe. Besides, the trifluoromethyl group of trifluoromethyl phenylboronic acid (2a) could detect 6mA modification through 19F NMR. Combined with this sensor system, 6mA modification could be detected well and quickly in 6 types of deoxynucleoside mixtures and DNA samples. Taken together, the method developed in the current study has potential for specific detection of 6mA in biological samples.

Two Gracilioethers Containing a [2(5H)-Furanylidene]ethanoate Moiety and 9,10-Dihydroplakortone G: New Polyketides from the Caribbean Marine Sponge Plakortis halichondrioides

Gracilioether M (6) and 11,12-dihydrogracilioether M (7), two polyketides with a [2(5H)-furanylidene]ethanoate moiety, along with known plakortone G (9) and its new naturally occurring derivative 9,10-dihydroplakortone G (8), were isolated from the Caribbean marine sponge Plakortis halichondrioides. The structures and absolute configuration of 6, 7, and 8 were characterized by analysis of HRESIMS and NMR spectroscopic data, chemical derivatization, and side-by-side comparisons with published NMR data of related analogs. Compounds 6 and 7 and a mixture of 8 and 9 were evaluated for cytotoxicity against MCF-7 human breast cancer cells. In addition, the in vitro antiplasmodial activity against Plasmodium berghei of these compounds was scrutinized using a drug luminescence assay.

High-sensitivity profiling of dipeptides in sauce-flavor Baijiu Daqu by chemical derivatization and ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry

Dipeptides in sauce-flavor Baijiu Daqu are protein degradation products during the fermentation of Daqu, which are believed to play a crucial role in the flavor and quality of Baijiu. Herein, we integrated dansyl chloride derivatization with ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) for comprehensively profiling dipeptides in Daqu. The derivatization efficiency was higher than 99.1 % for all 17 dipeptide standards under the optimized derivatization conditions. In total, 118 dipeptides were detected in Daqu. The method was validated and the analytical characteristics including the linearity (spanned across 2–4 orders of magnitude), precision (1.2–19.9 %), limit of detection (varied from 1.1 to 53.4 pmol/mL) and the stability (3.6–15.8 %) are satisfactory. The usefulness of the method was examined by studying the distribution characteristics of dipeptides in Daqu under different production conditions. The present method provides an effective and robust strategy for comprehensively analyzing dipeptide compounds in complex biological samples.

Mobilized Electrospray Device for On-Tissue Chemical Derivatization in MALDI-MS Imaging.

Applying solutions of a matrix or derivatization agent via microdroplets is a common sample preparation technique for matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) experiments. Mobilized nebulizer sprayers are commonly used to create a homogeneous matrix or reagent layer across large surfaces. Electrospray devices have also been used to produce microdroplets for the same purpose but are rarely used for large tissues due to their immobility. Herein, we present a movable electrospray device that can be used for large tissue sample preparation through a simple modification to an automatic commercial nebulizer device. As demonstrated for on-tissue chemical derivatization (OTCD) with Girard's reagent T using a mimetic tissue model, the sprayer has the additional benefit of being able to investigate reaction acceleration in OTCD when comparing electrostatically charged spray to electrostatically neutral spray. Finally, MALDI-MSI of fatty aldehydes is successfully demonstrated in rat brain tissues using this device for both OTCD and matrix application.

Trimethylation Enhancement Using Diazomethane (TrEnDi) Enables Enhanced Detection of Glufosinate and 3-(Methylphosphinico)propionic Acid from Complex Canola Samples.

Over the past century, agriculture practices have transitioned from manual cultivation to the use of an array of chemical herbicides for weed control including phosphinothricin, or glufosinate (GLUF). Consequently, the potential for long-term residual GLUF exposure in the food chain has increased, highlighting the need for improved analytical strategies for its detection, as well as the detection of its main breakdown product 3-(methylphosphinico)propionic acid (MPPA). Chemical derivatization strategies have been developed to improve the detection of GLUF and MPPA via liquid chromatography tandem mass spectrometry analyses. Herein, we employ trimethylation enhancement using diazomethane (TrEnDi) for the first time as a means to confer analytical advantages via quantitatively derivatizing these analytes into permethylated GLUF ([GLUFTr]+) and MPPA ([MPPATr+H]+). Comparing [GLUFTr]+ and [MPPATr+H]+ to underivatized counterparts, TrEnDi yields 2.8-fold and 1.7-fold improvements in reversed-phase chromatographic retention, respectively, while MS-based sensitivity is enhanced 4.1-fold and 11.0-fold, respectively. Successful analyte derivatization (with >99% yields) was further demonstrated on a commercial herbicide solution imparting consistent analytical enhancements. To investigate the benefits of TrEnDi in a bona fide agricultural scenario, simple aqueous extractions from distinct parts of field-grown canola plants were performed to quantify GLUF and MPPA before and after TrEnDi derivatization. In their underivatized forms, GLUF and MPPA were undetectable in all field samples, whereas [GLUFTr]+ and [MPPATr+H]+ were readily quantifiable using the same analysis conditions. Our results demonstrate that TrEnDi continues to be a useful tool to enhance the analytical characteristics of organic molecules that are traditionally difficult to detect.

Nature-Inspired Tetrahydropentalene Building Blocks: Scalable Synthesis for Medicinal Chemistry Needs

Inspired by the bioactivity of natural compounds with a bicyclo[3.3.0]octane core, the study focuses on developing tetrahydropentalene-2,5-dione (2,5-THP-dione) derivatives as potential building blocks for the use in medicinal chemistry. Using the commercially available 2,5-THP-dione, a number of alkylated derivatives and a monofunctional ketone were synthesized. Using optimized protocols for synthesis, target compounds were obtained with high yields on a multigram scale. These compounds are promising derivatives for further chemical derivatization and therapeutic use, and thus highlight the value of 2,5-THP-dione in creating complex molecular structures for drug discovery, as well as the importance of tetrahydropentalene derivatives as valuable building blocks in synthetic chemistry.

A chemical derivatization-based pseudotargeted liquid chromatography-tandem mass spectrometry method for sensitive and high coverage determination of bile acids in human serum

Global profiling of bile acids (BAs) is imperative for understand their function and disease pathogenesis. But it is still a challenging task, as the collision-induced dissociation (CID) fragment ions of unconjugated BAs showed low ion intensities to insufficient analysis. Herein, we developed a highly sensitive method for pseudotargeted profiling of BAs by chemical derivatization. In the developed method, a labeling reagent, 2-dimethylaminoethylamine (DMED), was adopted to label the carboxyl group of BAs. The results demonstrated that the detection sensitivities of unconjugated BAs were increased by 4–200 folds after DMED-labeling. Moreover, to profile other potential BAs not included in the 91 known targets, diverse survey experiments were performed on Qtrap-MS to search BAs for both precursor and fragment ion species, and retention index (RI) strategy was adopted to facilitate the identification of isomers. Finally, MRM-based LC-MS/MS method was validated for the pseudotargeted profiling of the BAs submetabolome with good linearity (r2 ≥ 0.990 for 89 known BAs) and high sensitivity (0.05–0.5 ng/mL for unconjugated BAs), covering unconjugated, glycine, taurine, sulfuric acid, glucuronic acid, and as well as those doubly-conjugated with above types. With this method, a total of 107 BAs, covering 54 BAs identified by authentic standards and 53 BAs candidates, were successfully determined in human serum of women with intrahepatic cholestasis of pregnancy (ICP). Multivariate analysis revealed deferentially expressed BAs. ICP disease altered the BAs profile with a reduced proportion of unconjugated, sulfate- and doubly-conjugated BAs and an increased proportion of glycine and taurine conjugates. Altered proportion and profile of BAs in ICP groups were gradually recovered during the ursodeoxycholic acid (UDCA) therapy. Overall, the strategy of DMED-labeling technique combined with diverse survey experiments is sufficiently sensitive and robust to comprehensively analysis of metabolic profiling of BAs in human serum.