Strategy to Empower Nontargeted Metabolomics by Triple-Dimensional Combinatorial Derivatization with MS-TDF Software.

Chemical derivatization is a widely employed strategy in metabolomics to enhance metabolite coverage by improving chromatographic behavior and increasing the ionization rates in mass spectroscopy (MS). However, derivatization might complicate MS data, posing challenges for data mining due to the lack of a corresponding benchmark database. To address this issue, we developed a triple-dimensional combinatorial derivatization strategy for nontargeted metabolomics. This strategy utilizes three structurally similar derivatization reagents and is supported by MS-TDF software for accelerated data processing. Notably, simultaneous derivatization of specific metabolite functional groups in biological samples produced compounds with stable but distinct chromatographic retention times and mass numbers, facilitating discrimination by MS-TDF, an in-house MS data processing software. In this study, carbonyl analogues in human plasma were derivatized using a combination of three hydrazide-based derivatization reagents: 2-hydrazinopyridine, 2-hydrazino-5-methylpyridine, and 2-hydrazino-5-cyanopyridine (6-hydrazinonicotinonitrile). This approach was applied to identify potential carbonyl biomarkers in lung cancer. Analysis and validation of human plasma samples demonstrated that our strategy improved the recognition accuracy of metabolites and reduced the risk of false positives, providing a useful method for nontargeted metabolomics studies. The MATLAB code for MS-TDF is available on GitHub at https://github.com/CaixiaYuan/MS-TDF.

Comments on "Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding".

In a recent communication (Angew. Chem. Int. Ed. 2024, 63, e202317312), Kalita et al. studied In4H+ system within the frame of single-reference approximation (SRA) and found that the global energy minimum (1 a) adopted the singlet state and a planar tetracoordinate hydrogen (ptH), while the second lowest isomer (1 b) located 3.0 kcal/mol above 1 a and adopted the triplet state as well as non-planar structure with a quasi-ptH. They assessed the reliability of SRA by checking the T1-diagnostic values of coupled cluster calculations. However, according to our multi-configurational second-order perturbation theory calculations at the CASPT2(12,13)/aug-cc-pVQZ (aug-cc-pVQZ-PP for In) level, both 1 a and 1 b exhibit obvious multi-referential characters, as reflected by their largest reference coefficients of 0.928 (86.1 %) and 0.938 (88.0 %), respectively. Moreover, 1 b is 5.05 kcal/mol lower than 1 a at this level, that is, what can be observed in In4H+ system is the quasi-ptH.

Research status and challenges of plant-derived exosome-like nanoparticles.

In recent years, there has been an increasing number of related studies on exosomes. Most studies have focused on exosomes derived from mammals, confirming the important role that exosomes play in cell communication. Plants, as a natural ingredient, plant-derived exosomes have been confirmed to have similar structures and functions to mammalian-derived exosomes. Plant-derived exosome-like nanoparticles (PELNs) are lipid bilayer membrane nanovesicles containing bioactive constituents such as miRNA, mRNA, protein, and lipids obtained from plant cells, that can participate in intercellular communication and mediate transboundary communication, have high bioavailability and low immunogenicity, are relatively safe, and have been shown to play an important role in maintaining cell homeostasis and preventing, and treating a variety of diseases. In this review, we describe the biogenesis, isolation and purification methods, structural composition, stability, safety, function of PELNs and challenges. The functions of PELNs in anti-inflammatory, antioxidant, antitumor and drug delivery are mainly described, and the status of research on exosome nanoparticles of Chinese herbal medicines is outlined. Overall, we summarized the importance of PELNs and the latest research results in this field and provided a theoretical basis for the future research and clinical application of PELNs.

CBe4H6: a molecular rotor with a built-in on-off switch.

It is highly challenging to control (stop and resume as needed) molecular rotors because their intramolecular rotations are electronically enabled by delocalized σ bonding, and the desired control needs to be able to destroy and restore such σ bonding, which usually means difficult chemical manipulation (substitution or doping atom). In this work, we report CBe4H6, a molecular rotor that can be controlled independently of chemical manipulation. This molecule exhibited the uninterrupted free rotation of Be and H atoms around the central carbon in first-principles molecular dynamics simulations at high temperatures (600 and 1000 K), but the rotation cannot be witnessed in the simulation at room temperature (298 K). Specifically, when a C-H bond in the CBe4H6 molecule adopts the equatorial configuration at 298 K, it destroys the central delocalized σ bonding and blocks the intramolecular rotation (the rotor is turned "OFF"); when it can adopt the axial configuration at 600 and 1000 K, the central delocalized σ bonding can be restored and the intramolecular rotation can be resumed (the rotor is turned "ON"). Neutral CBe4H6 is thermodynamically favorable and electronically stable, as reflected by a wide HOMO-LUMO gap of 7.99 eV, a high vertical detachment energy of 9.79 eV, and a positive electron affinity of 0.24 eV, so it may be stable enough for the synthesis, not only in the gas phase, but also in the condensed phase.

Luminescent lanthanide complexes based on 4,5-di(3,5-dicarboxylphenoxy)phthalic acid as enhanced fluorescence probes for highly selective detection of lead(II) ions in water.

Six novel lanthanide complexes ([Nd2(L)(H2O)6]n·4.58n(H2O) (1), [Ln(H3L)(H2O)]n·0.5n(H2O), Ln = Sm (2), Eu (3), Gd (4), Tb (5), Eu0.18Gd0.62Tb0.20 (6)) have been hydrothermally synthesized based on the ligand 4,5-di(3,5-dicarboxylphenoxy)phthalic acid (H6L). Single crystal X-ray diffraction reveals that complexes 1-6 are 2D structures, where 2-6 are isomorphic. Complexes 3 and 5 exhibit the characteristic fluorescence of Eu(III) and Tb(III) ions respectively, while complex 4 shows blue-green light emission based on the ligand. In particular, the ternary Eu/Gd/Tb complex 6 shows white light emission with a CIE (Commission International del'Eclairage) chromaticity coordinate of (0.330, 0.339) and hence close to pure white light emission. Moreover, complexes 3 and 5 display specific fluorescence-enhanced detection performance for Pb2+ ions: The interaction between Pb2+ ions and the ligand enhances the charge transfer efficiency between the ligand and the Eu(III) and Tb(III) ions and thus leads to fluorescence enhancement of complexes 3 and 5. More importantly, complex 3 exhibits the lowest detection limit of 4.72 nM for Pb2+ ions among the existing complex fluorescent probes. In addition, both complexes 3 and 5 show good performance for recycling and for the detection of Pb2+ in real water samples.

Toxic metabolites and metabolic soft spots of celastrol based on glutathione metabolic capture and high-resolution mass spectrometry.

BACKGROUND: Celastrol is known as one of the most medicinally valuable compounds. However, the pharmaceutical application of celastrol is significantly limited due to high toxicity, while there are few reports on the mechanism of toxicity. METHODS: This study searched for possible toxic metabolites through phase I in vitro metabolism and glutathione capture experiments. Then in vivo metabolism experiments in mice and rats were conducted to look for metabolites in vivo. Finally, mice in vivo toxicity experiment was conducted to verify the toxicity of different doses of celastrol to mice. RESULTS: In the in vivo and in vitro metabolism experiments, we found 7 phase I metabolites in vitro, 9 glutathione conjugation metabolites in vitro, and 20 metabolites in vivo. The metabolic soft points of celastrol could be the quinone methyl structure at C3-OH and C6. In vivo toxicity experiments show that celastrol causes weight loss, diarrhea, gastrointestinal tract and liver inflammation in mice. CONCLUSIONS: This study analyzed the metabolites and possible metabolic soft spots of celastrol, and its hepatotoxicity and gastrointestinal toxicity were demonstrated through in vivo studies for the first time. The results might provide an important basis for potential structural modification to increase the druggability of celastrol.

[(OB)2-M©B7O7-BO]- (M = Mn, Tc, Re): Chemically Stable and Triply Aromatic Ballet Rotors.

Single-molecule nanorotors are generally constructed based on boron atoms to obtain structural fluxionality via possessing the delocalized multicenter bonds. However, the electron-deficient boron atoms are commonly exposed in these nanorotors, which leads to extremely high chemical reactivity, which blocks the synthesis in the condensed phase. In this work, we computationally designed a series of transition-metal-doped boron oxide clusters MB10O10- (in structural configuration of [(OB)2-M©B7O7-BO]-, M = Mn, Tc, Re, © means "centered" in a planar or quasi-planar hypercoordinate environment), which can be vividly named as "ballet rotors" to label their anthropomorphic dynamic rotational behaviors. The rotational fluxionality in ballet rotors originates from the completely delocalized nature of the bonding within their MB10 core moieties. Remarkably, compared with single-molecule nanorotors having bare boron atoms and the narrow HOMO-LUMO gaps (≤4.00 eV) as well as low vertical detachment energies (VDEs, ≤4.46 eV for anions), the ballet rotors possess significantly improved chemical stability, as evidenced sterically by the absence of exposed boron atoms and electronically by much wider HOMO-LUMO gaps (5.66-5.98 eV) as well as obviously higher VDEs between 5.36 and 5.47 eV. Specifically, the ballet rotors are mainly stabilized by the delicately placed peripheral oxygen atoms, which can compensate for all electron-deficient boron atoms via O → B π back bonds and sterically protect them. Simultaneously, they are additionally stabilized by aromatic stabilization effect from possessing the novel S + P + D triple aromaticity. We expect that the proposal of chemically stable ballet rotors in this work can arouse the rational design of nanorotors for experimental realization in the condensed phase.

[Sc©[3]CPP]+: A Viable Metal-Centered [3]Cycloparaphenylene.

[n]Cycloparaphenylenes ([n]CPPs, n denotes the number of phenyl groups) are difficult to synthesize because of the strain related to their bent phenyl rings. In particular, the strain in [3]CPP is high enough to destroy the π electron delocalization, leading to the spontaneous structural transition to an energetically more stable "bond-shift" (BS) isomer ([3]BS). In this contribution, we propose to achieve [3]CPP by enhancing the π electron delocalization through hosting a guest metal atom. Our computations revealed that Sc could stabilize [3]CPP by forming the [Sc©[3]CPP]+ complex through the favorable π-Sc donation-backdonation interactions. Thermodynamically, the binding energy between the Sc atom and [3]CPP was -205.7 kcal/mol, which could well compensate not only the energy difference of 44.2 kcal/mol between [3]CPP and [3]BS but also the extremely high strain energy of 170.3 kcal/mol in [3]CPP. Simultaneously, the [Sc©[3]CPP]+ complex is stable up to 1500 K in dynamic simulations, suggesting its high viability in the synthesis.

NAl4X4 + (X = S, Se, Te): Clusters with a planar tetracoordinate nitrogen and significantly improved stability.

The design of clusters featuring non-classical planar hypercoordinate atoms (phAs) often depends on the delocalized multicenter bonds involving reactive electron-deficient elements, which both destabilize the clusters and lead to difficulty in achieving the phA arrangement for electronegative elements such as nitrogen due to their preference for localized bonds. In this work, we computationally designed a series of aluminum chalcogenide clusters NAl4X4 + (X = S, Se, Te) with a desired planar tetracoordinate nitrogen and meaningfully improved chemical stability, as evidenced by the wide gaps (6.51-7.23 eV) between their highest occupied molecular orbitals and lowest unoccupied molecular orbitals, high molecular rigidity (dynamically stable up to 1500 K), and exclusively low global energy minima nature (their isomers locate at least 51.2 kcal/mol higher). Remarkably, these clusters are stabilized by peripheral chalcogen atoms, which not only sterically protect the NAl4 core moiety but also electronically compensate for the electron-deficient aluminum atoms via X → Al π back bonds, meeting the description of our recently proposed "electron-compensation" strategy.

3-D molecular stars with covalent axial bonding.

In designing three-dimensional (3-D) molecular stars, it is very difficult to enhance the molecular rigidity through forming the covalent bonds between the axial and equatorial groups because corresponding axial groups will generally break the delocalized π bond over equatorial frameworks and thus break their star-like arrangement. In this work, exemplified by designing the 3-D stars Be2 ©Be5 E5 + (E = Au, Cl, Br, I) with three delocalized σ bonds and delocalized π bond over the central Be2 ©Be5 moiety, we propose that the desired covalent bonding can be achieved by forming the delocalized σ bond(s) and delocalized π bond(s) simultaneously between the axial groups and equatorial framework. The covalency and rigidity of axial bonding can be demonstrated by the total Wiberg bond indices of 1.46-1.65 for axial Be atoms and ultrashort Be-Be distances of 1.834-1.841 Å, respectively. Beneficial also from the σ and π double aromaticity, these mono-cationic 3-D molecular stars are dynamically viable global energy minima with well-defined electronic structures, as reflected by wide HOMO-LUMO gaps (4.68-5.06 eV) and low electron affinities (4.70-4.82 eV), so they are the promising targets in the gas phase generation, mass-separation, and spectroscopic characterization.

Magnetic chitosan/TiO2 composite for vanadium(v) adsorption simultaneously being transformed to an enhanced natural photocatalyst for the degradation of rhodamine B.

A magnetic chitosan/TiO2 composite material (MCT) was developed. MCT was successfully synthesized by a one-pot method using chitosan, TiO2, and Fe3O4. The absorption equilibrium time of MCT was 40 min in absorbing vanadium(v), the optimal adsorption pH was 4, and the maximum adsorption capacity of vanadium(v) was 117.1 mg g-1. The spent MCT was applied to photocatalytic reactions for reutilization. The decolorization rates for the degradation of rhodamine B (RhB) by new and spent MCT were 86.4% and 94.3%, respectively. The new and spent MCT exhibited absorption bands at 397 and 455 nm, respectively, which showed that the spent MCT was red-shifted to the cyan light region. These results indicated that the forbidden band widths of the new and spent MCT were about 3.12 and 2.72 eV, respectively. The mechanism of the degradation reaction showed that the hydroxyl radicals as oxidants in the spent MCT mediated the photocatalytic degradation of RhB. In addition, the superoxide anion radical formation of hydroxyl radicals was the main reaction, and the hole generation of hydroxyl radicals was the subordinate reaction. The N-de-ethylated intermediates and organic acids were monitored by MS and HPLC.

Syntheses and fluorescence properties of lanthanide isostructural complexes derived from aspartic acid.

To protect ecosystem balance and human health, the development of fluorescent sensing materials with high sensitivity and portability has attracted wide attention in several decades. Herein, six lanthanide isostructural complexes {[Ln(µ6-Hcaa)(H2O)]Cl}n (H3caa = N-(4-carboxylbenzyl)-L-aspartic acid, Ln3+ = Ce3+ (1), Pr3+ (2), Nd3+ (3), Sm3+ (4), Eu3+ (5), and Tb3+ (6)) with optical properties based on aspartic acid derivative (H3caa) were synthesized by the solvothermal method and characterized in detail. It is worth noting that complex 6 can not only specifically recognize Cr(VI) with very low detection limits (LODs) of 3.66 nM (Cr2O72-) & 5.35 nM (CrO42-) but also selectively recognize TCs with LODs of 0.24 µM (CTC = chlortetracycline) and 0.25 µM (TC = tetracycline) based on the method of fluorescence detection. In addition, the identification of Cr(VI) and TCs by visual colorimetry may be realized through the combination of a smartphone and portable test strips. This study suggests that complex 6 is a good optical material for detecting heavy metals and antibiotic contaminants in aqueous systems and broadens the development of amino acid derivatives.

Electron-compensation: a valid strategy for chemically stabilizing boron-based clusters with hypercoordinate centres.

To eliminate the chemical instability caused by the electron-deficiency of boron, two types of usual dative π bonds are recommended for compensating boron atoms in the computational design of boron-based clusters having hypercoordinate centres, which can lead to unusually stable targets for synthesis in the condensed phase.

Seven Ln(III) coordination polymers with two kinds of geometric coordination but the same 3D topological property: luminescence sensing and magnetic property.

Two series of seven lanthanide metal coordination polymers (Ln-CPs) formulated as {[Ln(dttpa)1.5(H2O)2]·H2O}n [Ln = La3+ (1), Ce3+ (2), Nd3+ (3), Sm3+ (4) and Eu3+ (5)] and {[Ln (dttpa)1.5(H2O)]·xH2O}n [Ln = Tb3+ (6) and Er3+ (7), x = 0.75] have been successfully constructed using Ln3+ ions and 2,5-di(1H-1,2,4-triazol-1-yl)terephthalic acid (H2dttpa) via a hydrothermal method. Their 3D structures are fully characterised by Fourier transform infrared (FT-IR) spectroscopy, X-ray single-crystal analyses, powder diffraction analyses (PXRD), elemental analyses (EAs) and thermogravimetric analyses (TGAs). All Ln-CPs display the same topological property with the point symbol of {42·84}{44·62}2{49·66}2, and crystallize in the triclinic space group P1̄. Interestingly, Eu-CP (5) effectively sensitizes the visible emission of Tb3+ and shows high selectivity and stable response with the lowest detection limit of 9.88 nM. Furthermore, Tb-CP (6) acts as a good luminescence sensor to detect nitrobenzene (NB) with a detection limit of 12.5 nM. In addition, the magnetic susceptibility measurement for Er-CP (7) further shows that compounds constructed by dttpa2- are a kind of promising functional material.

Planar pentacoordinate carbon in a sulphur-surrounded boron wheel: the global minimum of CB5S5.

We report a σ + π double aromatic CB5S5+ cluster, the first global minimum unusually having a planar hypercoordinate carbon inside a boron wheel. Five peripheral sulfur atoms stabilize the carbon-centered boron wheel by weakening the electron deficiency of the boron atoms through strong S → B π back-bonding.

Identification of potential anti-pneumonia pharmacological components of Glycyrrhizae Radix et Rhizoma after the treatment with Gan An He Ji oral liquid.

Glycyrrhizae Radix et Rhizoma, a traditional Chinese medicine also known as Gan Cao (GC), is frequently included in clinical prescriptions for the treatment of pneumonia. However, the pharmacological components of GC for pneumonia treatment are rarely explored. Gan An He Ji oral liquid (GAHJ) has a simple composition and contains GC liquid extracts and paregoric, and has been used clinically for many years. Therefore, GAHJ was selected as a compound preparation for the study of GC in the treatment of pneumonia. We conducted an in vivo study of patients with pneumonia undergoing GAHJ treatments for three days. Using the intelligent mass spectrometry data-processing technologies to analyze the metabolism of GC in vivo, we obtained 168 related components of GC in humans, consisting of 24 prototype components and 144 metabolites, with 135 compounds screened in plasma and 82 in urine. After analysis of the metabolic transformation relationship and relative exposure, six components (liquiritin, liquiritigenin, glycyrrhizin, glycyrrhetinic acid, daidzin, and formononetin) were selected as potential effective components. The experimental results based on two animal pneumonia models and the inflammatory cell model showed that the mixture of these six components was effective in the treatment of pneumonia and lung injury and could effectively downregulate the level of inducible nitric oxide synthase (iNOS). Interestingly, glycyrrhetinic acid exhibited the strongest inhibition on iNOS and the highest exposure in vivo. The following molecular dynamic simulations indicated a strong bond between glycyrrhetinic acid and iNOS. Thus, the current study provides a pharmaceutical basis for GC and reveals the possible corresponding mechanisms in pneumonia treatment.

Research Progress on Natural Compounds Exerting an Antidepressant Effect through Anti-inflammatory.

Depression is a common mental illness that belongs to the category of emotional disorders that causes serious damage to the health and life of patients, while inflammation is considered to be one of the important factors that cause depression. In this case, it might be important to explore the possible therapeutic approach by using natural compounds exerting an anti-inflammatory and antidepressant effect, which has not been systematically reviewed recently. Hence, this review aims to systematically sort the literature related to the mechanism of exerting an antidepressant effect through antiinflammatory actions and to summarize the related natural products in the past 20 years in terms of several inflammatory-related pathways (i.e., the protein kinase B (Akt) pathway, monoamine neurotransmitters (5-hydroxytryptamine and norepinephrine) (5-HT and NE), the nod-like receptor protein-3 (NLRP3) inflammasome, proinflammatory cytokines, neurotrophins, or cytokine-signaling pathways), which might provide a useful reference for the potential treatment of depression.

Prediction of heptagonal bipyramidal nonacoordination in highly viable [OB-M©B7O7-BO]- (M = Fe, Ru, Os) complexes.

Non-spherical distributions of ligand atoms in coordination complexes are generally unfavorable due to higher repulsion than for spherical distributions. To the best of our knowledge, non-spherical heptagonal bipyramidal nonacoordination is hitherto unreported, because of extremely high repulsion among seven equatorial ligand atoms. Herein, we report the computational prediction of such nonacoordination, which is constructed by the synergetic coordination of an equatorial hepta-dentate centripetal ligand (B7O7) and two axial mono-dentate ligands (-BO) in the gear-like mono-anionic complexes [OB-M©B7O7-BO]- (M = Fe, Ru, Os). The high repulsion among seven equatorial ligand B atoms has been compensated by the strong B-O bonding. These complexes are the dynamically stable (up to 1500 K) global energy minima with the HOMO-LUMO gaps of 7.15 to 7.42 eV and first vertical detachment energies of 6.14 to 6.66 eV (being very high for anions), suggesting their high probability for experimental realization in both gas-phase and condensed phases. The high stability stems geometrically from the surrounded outer-shell oxygen atoms and electronically from meeting the 18e rule as well as possessing the σ + π + δ triple aromaticity. Remarkably, the ligand-metal interactions are governed not by the familiar donation and backdonation interactions, but by the electrostatic interactions and electron-sharing bonding.

M©B7O7+ (M = Ni, Pd, Pt): aromatic molecular stars with a planar heptacoordinate transition metal.

The dynamically stable global minima M©B7O7+ (M = Ni, Pd, Pt) are interesting in that they possess σ-aromaticity alone within the B7M core moiety, which can be attributed to the strong peripheral localized O → B π back-bonding that leads to the less favourable delocalized M → B π back-bonding over the B7M core moiety.

Metabolomic Profiling of Poor Ovarian Response Identifies Potential Predictive Biomarkers.

Objective: To characterize the serum metabolomic profile and its role in the prediction of poor ovarian response (POR). Patients: Twenty-five women with normal ovarian reserve (24-33 years, antral follicle count [AFC] ≥5, anti-Müllerian hormone [AMH] ≥1.2 ng/ml) as the control group and another twenty-five women with POR (19-35 years, AFC <5, AMH < 1.2 ng/ml) as the study group were collected in our study. The serum levels of the women in both groups were determined from their whole blood by untargeted liquid chromatography-mass spectrometry (LC-MS). Multivariate statistical analysis and cell signal pathways analysis were used to reveal the results. Results: A total of 538 different metabolites were finally identified in the two groups. Tetracosanoic acid, 2-arachidonoylglycerol, lidocaine, cortexolone, prostaglandin H2,1-naphthylamine, 5-hydroxymethyl-2-furancarboxaldehyde, 2,4-dinitrophenol, and D-erythrulose1-phosphate in POR were significantly different from control as were most important metabolites in support vector machines (p <0.05). Metabolomic profiling, together with support vector machines and pathway analysis found that the nicotinate and nicotinamide metabolism pathway, including L-aspartic acid, 6-hydroxynicotinate, maleic acid, and succinic acid semialdehyde, was identified to have significant differences in POR women compared to control women, which may be associated with ovarian reserve. Conclusion: This study indicated that LC-MS-based untargeted metabolomics analysis of serum provided biological markers for women with POR. The nicotinate and nicotinamide metabolism pathway may offer new insight into the complementary prediction and therapeutic potential of POR. The functional associations of these metabolites need further investigation.