A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases.

The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.

Diastereomers of Steroidal Alkaloids with Cytotoxic Activities against Non-Small-Cell Lung Cancer from the Bulbs of Fritillaria sinica.

Eleven new steroidal alkaloids, along with nine known related compounds, were isolated from the bulbs of Fritillaria sinica. Seven pairs of diastereomers were identified, including six and four 20-deoxy cevanine-type steroidal alkaloid diastereomers with molecular weights of 413 and 415, respectively. Structures were elucidated based on spectroscopic data analysis, chemical derivatization, and single-crystal X-ray diffraction analysis. Compounds 5, 9, 11, 12, 16, and 20 exhibited significant in vitro cytotoxic activity against non-small-cell lung cancer with CC50 values from 6.8 ± 3.9 to 12 ± 5 µM.

Characterization of the natural peptidome of four leeches by integrated proteogenomics and pseudotargeted peptidomics.

Animal-derived drugs are an indispensable part of folk medicine worldwide. However, their chemical constituents are poorly approached, which leads to the low level of the quality standard system of animal-derived drugs and further causes a chaotic market. Natural peptides are ubiquitous throughout the organism, especially in animal-derived drugs. Thus, in this study, we used multi-source leeches, including Hirudo nipponica (HN), Whitmania pigra (WP), Whitmania acranulata (WA), and Poecilobdella manillensis (PM), as a model. A strategy integrating proteogenomics and novel pseudotargeted peptidomics was developed to characterize the natural peptide phenotype and screen for signature peptides of four leech species. First, natural peptides were sequenced against an in-house annotated protein database of closely related species constructed from RNA-seq data from the Sequence Read Archive (SRA) website, which is an open-sourced public archive resource. Second, a novel pseudotargeted peptidomics integrating peptide ion pair extraction and retention time transfer was established to achieve high coverage and quantitative accuracy of the natural peptides and to screen for signature peptides for species authentication. In all, 2323 natural peptides were identified from four leech species whose databases were poorly annotated. The strategy was shown to significantly improve peptide identification. In addition, 36 of 167 differential peptides screened by pseudotargeted proteomics were identified, and about one-third of them came from the leucine-rich repeat domain (LRR) proteins, which are widely distributed in organisms. Furthermore, six signature peptides were screened with good specificity and stability, and four of them were validated by synthetic standards. Finally, a dynamic multiple reaction monitoring (dMRM) method based on these signature peptides was established and revealed that one-half of the commercial samples and all of the Tongxinluo capsules were derived from WP. All in all, the strategy developed in this study was effective for natural peptide characterization and signature peptide screening, which could also be applied to other animal-derived drugs, especially for modelless species that are less studied in protein database annotation.

Fingerprinting Evaluation and Gut Microbiota Regulation of Polysaccharides from Jujube (Ziziphus jujuba Mill.) Fruit.

Jujube fruit was well-loved and praised by the broad masses due to its delicious taste, abundant nutritional value, and medicinal properties. Few studies reported the quality evaluation and gut microbiota regulation effect of polysaccharides of jujube fruits from different producing areas. In the present study, multi-level fingerprint profiling, including polysaccharides, oligosaccharides, and monosaccharides, was established for the quality evaluation of polysaccharides from jujube fruits. For polysaccharides, the total content in jujube fruits ranged from 1.31% to 2.22%, and the molecular weight distribution (MWD) ranged from 1.14 × 105 to 1.73 × 106 Da. The MWD fingerprint profiling of polysaccharides from eight producing areas was similar, but the profile of infrared spectroscopy (IR) showed differentiation. The characteristic signals were screened and used to establish a discrimination model for the identification of jujube fruits from different areas, and the accuracy of identification reached 100.00%. For oligosaccharides, the main components were galacturonic acid polymers (DP, 2-4), and the profile of oligosaccharides exhibited high similarity. The monosaccharides, GalA, Glc, and Ara, were the primary monosaccharides. Although the fingerprint of monosaccharides was semblable, the composing proportion of monosaccharides revealed significant differences. In addition, the polysaccharides of jujube fruits could regulate the gut microbiota composition and possess potential therapeutic effects on dysentery and nervous system diseases.

Determination of six core components from Mahuang Xuanfei Zhike syrup in rat plasma and tissues by UPLC-MS/MS: Application to a pharmacokinetics and tissue distribution study.

Mahuang Xuanfei Zhike (MXZ) syrup, a Chinese patent medicine, has been widely used in the clinical treatment of cough. However, there is no reported method for the quantitative analysis of the effective components of MXZ syrup in biological samples. In this study, the effective components of MXZ syrup were screened by network pharmacology and molecular docking technology. A sensitive and rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was established to test the active components of MXZ syrup in rat plasma and tissue homogenates, including ephedrine, amygdalin, chlorogenic acid, harpagoside, forsythin and forsythoside A. Chromatographic separation was performed on a Waters Acquity UPLC HSS T3 column (2.1 × 50 mm, 1.8 µm) and the mass analysis was conducted using a Waters Xevo TQ mass spectrometer using multiple reaction positive and negative ion simultaneous monitoring mode. The results showed that the linearity ranged from 0.3 to 409.4 ng/ml. The extraction recoveries were all <8.33%, and the matrix effects were all <8.45, which met the requirements. The pharmacokinetic and tissue distribution results indicated that the main active components of MXZ syrup were absorbed quickly and eliminated slowly in vivo, and there may be a reabsorption process.

Systematical characterization and comparison of saponins in Achyranthes bidentata Blume and its three analogous species.

INTRODUCTION: Achyranthes bidentata Blume (AB) has been used for a long time and is recorded in the Chinese Pharmacopoeia 2020 edition. It is commonly confused with Achyranthes aspera Linn (AA), Cyathula officinalis Kuan (CO) and Cyathula capitata (Wall.) Moq. (CC), belonging to the Achyranthes and Cyathula genera of the Amaranthaceae family. It is of great significance to recognize and distinguish chemical components of AB, AA, CO and CC. OBJECTIVE: The purpose of this study was to develop an analytical method for in-depth characterization and comparison of saponins in AB, AA, CO and CC. METHODS: The extracts of AB, AA, CO and CC were analyzed by an RP × RP (C18 × Phenyl-Hexyl) 2D LC system, eluted by acidic × ion pair mobile phases and detected by high resolution mass spectrometry. Fragmentation patterns of saponins were elucidated and proposed according to reference compounds or literature reports. RESULTS: As a result, 839 saponins consisting of 81, 415, 99 and 392 components corresponding to AB, AA, CO and CC, respectively, were characterized, including 594 potentially new saponins. Meanwhile, 29 kinds of aglycones were elucidated, among which 25 were new ones. Besides, 14, 91, 37 and 174 characteristic potential quality markers with MS intensities exceeding 10,000 were found in AB, AA, CO and CC, respectively. CONCLUSION: This comprehensive study not only expands our knowledge of the types of saponins in Achyranthes and Cyathula, but also reveals the differences among four kinds of analogous herbs (AB, AA, CO and CC), which facilitates the quality control of these herbal medicines in the future.

Software Assisted Multi-Tiered Mass Spectrometry Identification of Compounds in Traditional Chinese Medicine: Dalbergia odorifera as an Example.

The complexity of metabolites in traditional Chinese medicine (TCM) hinders the comprehensive profiling and accurate identification of metabolites. In this study, an approach that integrates enhanced column separation, mass spectrometry post-processing and result verification was proposed and applied in the identification of flavonoids in Dalbergia odorifera. Firstly, column chromatography fractionation, followed by liquid chromatography-tandem mass spectrometry was used for systematic separation and detection. Secondly, a three-level data post-processing method was applied to the identification of flavonoids. Finally, fragmentation rules were used to verify the flavonoid compounds. As a result, a total of 197 flavonoids were characterized in D. odorifera, among which seven compounds were unambiguously identified in level 1, 80 compounds were tentatively identified by MS-DIAL and Compound Discoverer in level 2a, 95 compounds were annotated by Compound discoverer and Peogenesis QI in level 2b, and 15 compounds were exclusively annotated by using SIRIUS software in level 3. This study provides an approach for the rapid and efficient identification of the majority of components in herbal medicines.

[Analysis of chemical constituents in classical prescription Danggui Buxue Decoction based on RP-Q-TOF-MS and HILIC-Q-TOF-MS].

The chemical constituents of classical prescription Danggui Buxue Decoction were analyzed by reversed-phase(RP) chromatography and hydrophilic interaction chromatography(HILIC) coupled with quadrupole time-of-flight mass spectrometry. RP separation of Danggui Buxue Decoction was performed on ACQUITY UPLC HSS T3(2.1 mm×100 mm, 1.8 µm), while HILIC separation was on Waters BEH Amide(2.1 mm×100 mm, 1.7 µm). Mass spectrometry(MS) data were acquired in both negative and positive ion modes. Chemical constituents of Astragali Radix and Angelicae Sinensis Radix were searched from Reaxys and thus the in-house library was established. MS data were further analyzed by MassLynx 4.1 combined with in-house library, HMDB, Reaxys, and comparison with reference substances. In conclusion, a total of 154 compounds were identified and characterized: 16 saponins, 44 flavonoids, 10 phthalides, 7 phenylpropanoids, 15 bases and the corresponding nucleosides, 30 oligosaccharides, and 32 other compounds. Among them, 65 compounds were detected by HILIC-MS/MS. This study provides experimental evidences for the material basis research, quality control, and preparation development of Danggui Buxue Decoction and a reference method for comprehensive characterization of Chinese medicine decoctions typified by classical prescriptions.

[Identification of chemical constituents of Xiaochengqi Decoction by UPLC-Q-TOF/Fast DDA combined with UNIFI software].

Based on the combination of ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF) and Waters UNIFI software, the chemical constituents of the classic prescription Xiaochengqi Decoction were qualitatively analyzed and identified. The UPLC conditions are as follows: Acquity HSS T3 reverse phase column(2.1 mm ×100 mm, 1.8 µm), column temperature of 30 ℃, mobile phase of 0.1% formic acid aqueous solution(A)-acetonitrile(B), and flow rate of 0.3 mL·min~(-1). High-resolution MS data of Xiaochengqi Decoction were collected in ESI~(+/-) modes by Fast DDA. The structures of the chemical constituents were tentatively characterized or identified by UNIFI software according to the retention time of reference standards and characteristic fragment ions in MS profile, and literature data. A total of 233 components in Xiaochengqi Decoction were identified, with 93 from wine-processed Rhei Radix et Rhizoma, 104 from bran-processed Aurantii Fructus Immaturus, and 36 from ginger-processed Magnoliae Officinalis Cortex. These 233 components included anthraquinones, flavonoids, lignans, alkaloids, coumarins, and phenylethanoid glycosides. The result provided experimental evidence for the further study on establishment of quality standard and product development of the formula.

Traditional Chinese medicine (TCM) as a source of new anticancer drugs.

Covering: up to July 2020Drugs derived from traditional Chinese medicine (TCM) include both single chemical entities and multi-component preparations. Drugs of both types play a significant role in the healthcare system in China, but are not well-known outside China. The research and development process, the molecular mechanisms of action, and the clinical evaluation associated with some exemplificative anticancer drugs based on TCM are discussed, along with their potential of integration in western medicine.

"Force iteration molecular designing" strategy for the systematic characterization and discovery of new protostane triterpenoids from Alisma Rhizoma by UHPLC/LTQ-Orbitrap-MS.

Comprehensive analysis and identification of chemical components are of great significance for evaluating the efficacy and safety of herbal medicines, as well as for drug exploitation and development. Here we developed a "force iteration molecular designing" strategy, by combing a database-based in-house software for a precursor ion list (PIL) and PIL-triggered collision-induced dissociation-MS2 and high-energy C-trap dissociation-MS2 (PIL-CID/MS2-HCD/MS2) on an LTQ-Orbitrap mass spectrometer, aiming for the systematic characterization and discovery of new protostane triterpenoids (PTs) from Alisma Rhizoma (AR). AR was a well-known herbal remedy widely used for diarrhea, but its systematic characterization and comparison between two botanical origins have not been reported. Firstly, in-house software was developed based on force iteration, to generate a PIL that contains 483 accurate precursor ions. Secondly, to facilitate the acquisition of rich fragments and diagnostic ions sufficient for the structural elucidation of different types of PTs, a hybrid data acquisition method, namely PIL-CID/MS2-HCD/MS2, was generated. Thirdly, a total of 473 PTs were rapidly characterized from two botanical origins of AR according to an established four-step interpretation method, and the common constituents were 277 with ratio 70% (277/395) and 78% (277/355) in the rhizome of Alisma plantago-aquatica and A. orientale, respectively. Finally, two new PTs were isolated and unambiguously identified by NMR verifying the feasibility of this combined data acquisition strategy. This integrated strategy could improve the efficiency in the detection of new compounds in a single run and is practical to comprehensively characterize the complex components in herbal medicines.

Nontargeted metabolomic analysis and multiple criteria decision-making method induced robust quality markers screening for the authentication of herbal medicines from different origins by taking Ophiopogon japonicus (L. f.) Ker-Gawl. as a case study.

A key segment in medicinal plant authentication is the establishment of quality markers that embody the intrinsic metabolites difference independent of instruments and experiment conditions. A strategy integrating nontargeted metabolomics and multicriteria decision-making model for robust quality markers discovery is presented and applied to authenticate Ophiopogon japonicus (L. f.) Ker-Gawl. First, an ultra-performance liquid chromatography/quadrupole time-of-flight MSE approach was established for global metabolites profiling and identification. Second, multivariate statistical analysis was performed to explore potential quality markers of different origins of ophiopogonis radix. Third, potential quality markers were ordered and filtered by multicriteria decision-making model to infer robust quality markers and further validated in different instruments and experiment conditions by validation model. Fourth, the validation model using the robust quality markers managed to discriminate the origins of ophiopogonis radix samples procured from the herbal markets. Consequently, two robust quality markers, cixi-ophiopogon B and ophiopogonin D, were discovered and further validated on different instruments and experiment conditions. This integrated strategy provided a practical solution for reliable and convenient authentication of geo-authentic herb.

Systematic characterization of chemical constituents in Mahuang decoction by UHPLC tandem linear ion trap-Orbitrap mass spectrometry coupled with feature-based molecular networking.

Comprehensive characterization of traditional Chinese medicine prescriptions has long been a hurdle due to the chemical complexity and the lack of analytical tools. Mahuang decoction is a well-known traditional Chinese medicine prescription widely used for sweating and relieving the exterior, relieving cough and asthma, but it was insufficiently chemically scrutinized. In this study, the chemical component information of Mahuang decoction was investigated by ultrahigh-performance liquid chromatography tandem linear ion trap-Orbitrap mass spectrometry. A new data processing tool, feature-based molecular networking, was introduced for grouping and elucidating the compounds. In this way, 156 chemical components were identified or tentatively characterized, including alkaloids, triterpenoid saponins, flavanone-O-glycosides, flavone-C-glycosides, and procyanidins. Thus, this research provides a solid foundation for further development of Mahuang decoction, and the adopted method is expected to be applied to other traditional Chinese medicine prescriptions.

A strategy for practical authentication of medicinal plants in traditional Chinese medicine prescription, paeony root in ShaoYao-GanCao decoction as a case study.

Authentication of Chinese medicine materials in prescriptions is extremely difficult due to the complicated chemical matrix. A strategy integrating in-depth profiling, chemical marker selection, and selected detection was established and exemplarily applied to authenticate paeony root in ShaoYao-GanCao decoction. First, an ultra-performance liquid chromatography/linear trap quadrupole-Orbitrap method was developed to probe the chemical compositions of the decoction. Second, 20 batches of decoctions prepared from white paeony root and red paeony root were compared by a metabolomics method, and multistep chemometrics analysis distinguished the chemical markers. Third, an ultra-performance liquid chromatography/QDa-selected ion monitoring method was developed to authenticate the paeony root in decoctions. As a result, 161 compounds were characterized, including 84 triterpene saponins, 42 flavonoids, and 10 monoterpenes. Four chemical markers and paeoniflorin were successfully screened out as chemical markers for white paeony root. The selected ion monitoring method easily differentiated authentic decoction (prepared from white paeony root) from fraud decoction (prepared from red paeony root) by monitoring the above five chemical markers. In conclusion, the strategy was proved effective in authentication of paeony root in ShaoYao-GanCao decoction, and it can also be applied to authenticate other Chinese medicine materials in prescriptions, which will greatly avail the quality enhancement of prescriptions.

Systematic comparison of metabolic differences of Uncaria rhynchophylla in rat, mouse, dog, pig, monkey and human liver microsomes.

Metabolites have a close relationship with the efficacy and safety of herbal medicines. However, ubiquitous matrix interferences, complex co-elution, and minor or trace amounts in plasma restrict the comprehensive identification of metabolites. In this study, an efficient strategy comprising a mass defect filter and time-staggered targeted ion lists was established to characterize the metabolites of alkaloids of Uncaria rhynchophylla (UR) for the systematic comparison of metabolic differences in rat, mouse, dog, pig, monkey and human liver microsomes. The mass defect filter model effectively decreased interfering ions by 63-68%, and time-staggered precursor ion lists significantly increased the number of triggered MS/MS fragmentation by 65-120% in liver microsomes of six species. Ultimately, a total of 165 metabolites in the liver microsomes of six species were tentatively characterized, and the main metabolic pathways were demethylation, isomerization, hydrolysis, oxygenation and dehydrogenation. The results showed that the mouse liver microsomes exhibited metabolic behavior most similar to human metabolism of UR alkaloids. We hope that these results provide basic data for further investigation of UR metabolism in different species, and that the strategy can provide a reference for metabolite characterization of herbal medicines in complex biological matrix. Graphical abstract.

A metabolomics strategy for authentication of plant medicines with multiple botanical origins, a case study of Uncariae Rammulus Cum Uncis.

Source authentication of herbal medicines was essential for ensuring their safety, efficacy and quality consistency, especially those with multiple botanical origins. This study proposed a metabolomics strategy for species discrimination and source recognition. Uncariae Rammulus Cum Uncis, officially stipulating the stems with hooks of five Uncaria species as its origins, was taken as a case study. Firstly, an untargeted MSE method was developed by ultra-high performance liquid chromatography hyphenated with quadrupole time-of-flight mass spectrometry for global metabolite characterization. Subsequently, data pretreatment was conducted by using Progenesis QI software and screening rules. The obtained metabolite features were defined as variables for statistical analyses. Principal component analysis and chemical fingerprinting spectra suggested that five official species were differentiated from each other except for Uncaria hirsuta and Uncaria sinensis. Furthermore, orthogonal partial least squares discrimination analysis was performed to discriminate confused two species, and resulted in the discovery of nine contributing markers. Ultimately, a Support Vector Machine model was developed to recognize five species and predict origins of commercial materials. The study demonstrated that the developed strategy was effective in discrimination and recognition of confused species, and promising in tracking botanical origins of commercial materials.

Two New Aristolochic Acid Analogues from the Roots of Aristolochia contorta with Significant Cytotoxic Activity.

Twelve compounds, including two new aristolochic acid analogues with a formyloxy moiety (9-10) and 10 known aristolochic acid derivates (1-8 and 11-12), were obtained from the roots of Aristolochiacontorta. Their structures were elucidated using extensive spectroscopic methods. Their cytotoxic activity in human proximal tubular cells HK-2 was evaluated by the MTT method, which has been widely used to assess cell viability. Among these molecules, compounds 3 and 9 were found to be more cytotoxic. Furthermore, molecular modeling was used to evaluate, for the first time, the interactions of compounds 3 and 9 with the target protein organic anionic transporter 1 (OAT1) that plays a key role in mediating aristolochic acid nephropathy. Structure-activity relationships are briefly discussed.

Implementation of a Single Quadrupole Mass Spectrometer for Fingerprint Analysis: Venenum bufonis as a Case Study.

The mass spectrometry (MS) has been widely used for profiling chemical components of traditional Chinese medicine (TCM). However, there are few studies reporting quality control of TCM based on mass spectrometry fingerprint (MSF) due to its complicated operation and high cost. The aim of this study was to extend the application of MSF for quality evaluation of TCM. In this study, an MSF based on single quadrupole mass spectrometry method was established, and was successfully used for the quality control of Venenum bufonis (VB), a famous TCM which was used clinically for cancer treatment in China. The results showed that the superiority of MSF for more chemical information exposure and the finding of more potential chemical markers (eight versus four) compared with the traditional photo-diode array (a kind of ultra violet detector, PDA). Besides, the performance of MSF was also validated by similarity and principle component analysis (PCA) of MS data acquired on two other mass spectrometry (low-resolution, triple quadrupole, QQQ, and high-resolution, quadruple time-of-flight, Q-TOF), showing high consistency with QQQ and Q-TOF, but robustness with few parameters' settings. Based on our study, MSF could be widely applied for the quality control of TCM.

Malonylginsenosides with Potential Antidiabetic Activities from the Flower Buds of Panax ginseng.

LC-MS-guided phytochemical isolation of malonylginsenosides, featuring neutral elimination of CO2 and C3H2O3 by the negative mode collision-induced dissociation, from the flower buds of Panax ginseng led to the isolation of 19 malonyl-substituted triterpenoid saponins. They include 15 new malonylginsenosides, malonylfloralginsenosides-Re1-Re3 (1-3), -Rb1 and -Rb2 (4, 5), -Rd1-Rd6 (6-11), and -Rc1-Rc4 (12-15), and the known m-Rb1, m-Rc, m-Rb2, and m-Rd (16-19). Compound 11 represents the first dimalonyl saponin isolated from the Panax genus, while 2-4, 9, and 10 are five ginsenosides with single malonylation at the C-20 sugar chain. The antidiabetic activities of nine of these malonyl-substituted ginsenosides (1, 3, 4, 8, 13, and 16-19) and five of the corresponding non-malonyl ginsenosides (Re, Rb1, Rb2, Rc, and Rd) were evaluated by L6 myotubes' glucose consumption and AMPKα2ß1γ1 activation. Ginsenoside Rb2, 1, and 18 promoted glucose consumption of differentiated L6 myotubes, while ginsenosides Rb1, Rb2, and Rd and the malonylginsenosides 4, 8, 13, 16, 17, and 19 activated AMPKα2ß1γ1 (EC50: 0.0168-2.8 µM, fold: 1.7-4.7).

UHPLC-Q-TOF-MS-based metabolomics approach to compare the saponin compositions of Xueshuantong injection and Xuesaitong injection.

Various traditional Chinese medicine preparations developed from Notoginseng total saponins, including Xueshuantong injection and Xuesaitong injection, are extensively used in China to treat cardiocerebrovascular diseases. However, the difference of their saponin compositions remains unknown. An ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry based metabolomics approach was developed to probe the saponin discrimination between Xueshuantong and Xuesaitong and the related factors by large sample analysis. A highly efficient chromatographic separation was achieved on an HSS T3 column within 20 min with the holistic metabolites information recorded in the negative MSE mode. A six-step data pretreatment procedure mainly based on Progenesis QI and mass defect filtering was established. Pattern recognition chemometrics was used to discover the potential saponin markers. The saponin composition of Wuzhou Xueshuantong showed distinct discrimination from the other products. Wuzhou Xueshuantong contains more abundant protopanaxatriol-type noto-R1 , Rg1 , Re, and protopanaxadiol-type Rb1 , but less Rd and other low-polarity protopanaxadiol-type ginsenosides. These differences could not directly correlate to the use of different parts of Panax notoginseng, but possibly to the different preparation techniques employed by different manufacturers. These results are beneficial to the establishment of pharmacopoeia standards and the assessment of the efficacy and adverse drug reactions for these homologous products.