Pharmacodynamical research of extracts and compounds in traditional Chinese medicines for Parkinson's disease.

Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease (AD). Currently, there is no cure for PD, and medications can only control the progression of the disease. Various experimental studies have shown the significant efficacy of TCM in treating PD, and combination with western medicine can enhance the effects and reduce toxicity. Thus, exploring effective anti-PD compounds from TCM has become a popular research fields. This review summarizes commonly used TCM extracts and natural products for the treatment of PD, both domestically and internationally. Furthermore, it delves into various mechanisms of TCM in treating PD, such as anti-oxidative stress, anti-inflammatory, anti-apoptotic, improve mitochondrial dysfunction, inhibits α-synuclein (α-Syn) misfolding and aggregation, regulating neurotransmitters, regulates intestinal flora, enhances immunity, and so on. The results reveal that most TCMs exert their neuroprotective effects through anti-inflammatory and anti-oxidative stress actions, thereby slowing down the progression of the disease. These TCM may hold the key to improving PD therapy and have tremendous potential to be developed as novel anti-PD drugs.

Intelligent chemical profiling of 73 edible flowers by liquid chromatography-high resolution mass spectrometry combined with HRMS database and their authentication based on large-scale fingerprints.

A commercial high-resolution MS database "TCM-PCDL" was innovatively introduced to automatically identify multi-components in 73 edible flowers rapidly and accurately by liquid chromatography-high resolution mass spectrometry, which can be time-consuming and labor-intensive in traditional manual method. The database encompasses over 2565 natural products with various energy levels. Unknown compounds can be identified through direct matching and scoring MS2 spectra with database. A total of 870 compounds were identified from 73 flowers, with polyphenols constituting up to 75%. Focusing on polyphenols, a high performance liquid chromatography (HPLC) method was developed to generate fingerprints from 510 batches, establishing an "HPLC database" that enabled accurate authentication using similarity scores and rankings. This method demonstrated an accuracy rate of 100% when applied to 30 unknown samples. For flowers prone to confusion, additional statistical analysis methods could be employed as aids in authentication. This study provides valuable insights for large-scale sample chemical profiling and authentication.

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.

Species discrimination of multiple botanical origins of Fritillaria species based on infrared spectroscopy, thin layer chromatography-image analysis and untargeted metabolomics.

BACKGROUND: Fritillaria Bulbus (FB), a precious medicinal herb renowned for its heat-clearing, lung-moistening, cough-relieving and phlegm-eliminating effects. In pursuit of profits, unscrupulous merchants have engaged in the substitution or adulteration of valuable varieties with cheaper alternatives. It is, therefore, urgent to develop effective technical approaches to identify FBs from adulterants. METHODS: This paper employed infrared spectroscopy (IR), thin layer chromatography-image analysis (TLC-IA), and untargeted metabolomics techniques to discriminate ten species of FBs. RESULTS: Five species of FBs were successfully differentiated using mid-infrared spectroscopy. Furthermore, the power of TLC-IA technology allowed the differentiation of five species of FBs and two origins of FCBs (Fritillariae Cirrhosae Bulbus). Remarkably, through the application of untargeted metabolomics technique, the precise discrimination of five species of FBs, as well as three origins of FCBs were accomplished. Moreover, a comprehensive identification of 101 markers that reliably distinguished diverse FBs was achieved through the employment of untargeted metabolomics technique. CONCLUSION: The investigation presented powerful means of detection for assuring the quality control of Fritillaria herbs.

MATLAB language assisted data acquisition and processing in liquid chromatography Orbitrap mass spectrometry: Application to the identification and differentiation of Radix Bupleuri from its adulterants.

Comprehensive and rapid analysis of secondary metabolites like saponins remains challenging. This study aimed to establish a semi-automated workflow for filtration, identification, and characterization of saikosaponins in six Bupleurum species. Radix Bupleuri, a high-sales herbal medicine, is often adulterated, restricting its quality control and applications. Two authentic Radix Bupleuri species and four major adulterants were analyzed through UHPLC-LTQ-Orbitrap-MS for targeted saikosaponin analysis. To reveal trace saikosaponins and obtain quality fragment data, a MATLAB-based process automatically enumerating "sugar chain + aglycone + side chain" combinations and deduplicating generated a predicted saikosaponin database covering all possible saikosaponins as a precursor ion list for comprehensive targeted acquisition. To focus on informative ions and reduce MS analysis workload, we utilized MATLAB to automatically filtrate the false positive ions by MS1 and MS2 spectrometry. The newly established MATLAB-assisted data acquisition approach exhibited 50 % improvement in characterization of targeted saikosaponins. Furthermore, positive and negative ionization workflows were designed for accurate saikosaponins characterization based on fragmentation rules. In total, 707 saikosaponins were characterized, including over 500 potential new compounds and previously unreported C29 aglycones. We identified 25 saikosaponins present in both authentic species but absent in adulterants as potential markers. This unprecedented comprehensive multi-origin species differentiation demonstrates the promise of MATLAB-assisted acquisition and processing to advance saponin identification and standardize the Radix Bupleuri market.

Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics.

Pheretima, also called "earthworms", is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines (CPMs) in Chinese Pharmacopoeia (2020 edition). However, its zoological origin is unclear, both in the herbal market and CPMs. In this study, a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms (restricted search, open search, and de novo) was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima, including Pheretima aspergillum (PA), Pheretima vulgaris (PV), and Metaphire magna (MM). We identified 10,477 natural peptides in the PA, 7,451 in PV, and 5,896 in MM samples. Five specific signature peptides were screened and then validated using synthetic peptides; these demonstrated robust specificity for the authentication of PA, PV, and MM. Finally, all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills, revealing the inconsistent Pheretima species used in these CPMs. In conclusion, our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines, especially non-model species with poorly annotated protein databases.

Undescribed steroidal alkaloids from the bulbs of Fritillaria sinica.

Eight undescribed steroidal alkaloid derivatives, including three cevanine-type isosteroidal alkaloids (two N-oxide glycosides and one D-ring aromatization) (1-3), one verazine-type steroidal alkaloid derivative (4), three solanidine-type steroidal alkaloid glycosides (5-7), and one veratramine-type analogue (8), along with three known compounds (9-11) were isolated from the bulbs of Fritillaria sinica. Their structures were elucidated by comprehensive analysis of spectroscopic data, acidic hydrolysis, and X-ray crystal diffractions. In the in vitro bioassay, the anti-cancer effect, anti-oxidation and anti-inflammatory activities for the isolates were evaluated at a concentration of 10 µM.

A novel integrated automatic strategy for amino acid composition analysis of seeds from 67 species.

The composition and quantity of amino acids (AAs) in seeds are complicated due to the various origins and modifications of different species. In this study, a novel automatic neutral loss filtering (ANLF) strategy based on accurate mass searching by Python was developed to analyze the free and hydrolyzed AA-phenyl isothiocyanate (PITC) derivatives from seeds of Gymnosperm and Angiosperm phyla. Compared with traditional strategies, ANLF showed much higher accuracy in screening AA derivatives by filtering nitrogen-containing non-AA compounds and efficiency in processing large datasets. Meanwhile, the content phenotype of 20 proteinogenic AAs from seeds of these two families was characterized by a 35-min HPLC method combined with an automated peak-matching strategy. AA profiles of 232 batches of seeds from 67 species, consisting of 19 proteinogenic AAs, 21 modified AAs, and 77 unknown AAs, would be a good reference for their application in food and medicine.

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.

Systematical characterization of gypenosides in Gynostemma pentaphyllum and the chemical composition variation of different origins.

Gynostemma pentaphyllum (Thunb.) Makino is an herbaceous plant of Cucurbitaceae family, which has been widely used as an herbal tea and traditional Chinese medicine. Since its saponins are similar to ginsenosides and have a wide range of activities, it has attracted wide interest. However, there are still a large number of unknown saponins that have not been isolated, especially some trace gypenosides. In the present study, a HILIC × RP offline two-dimensional liquid separation combined with a multimode data acquisition was developed for the systematical characterization of gypenosides. On top of the negative mode information, considering that saponins are prone to in-source fragmentations in positive ion mode, a precursor ion list data acquisition method was used for the targeted acquisition of multistage positive data. Reference herbal drug was taken as a golden sample to probe the chemical composition of G. pentaphyllum. The mixed sample of commercially available samples were also analyzed in parallel. Furthermore, the chemical compositions of commercially available samples from different sources were compared. In total, 1108 saponins were characterized, among which 588 were accurately characterized, with 574 identified in the reference herbal drug and 700 in the mixed commercially available samples. The commercially available samples showed great composition variation. These findings clarified the material basis and provided clues for quality control of G. pentaphyllum.

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.

Identification of Five Gelatins Based on Marker Peptides from Type I Collagen by Mass Spectrum in Multiple Reaction Monitoring Mode.

In this study, a novel pseudo-targeted peptidomics strategy, integrating the transition list generated by an in-house software (Pep-MRMer) and the retention time transfer by high-abundance ion-based retention time calibration (HAI-RT-cal), was developed to screen marker peptides of gelatins from five closely related animal species, including porcine, bovine, horse, mule, and donkey. Five marker peptides were screened from the molecular phenotypic differences of type I collagen. Furthermore, a simple and robust 10 min multiple reaction monitoring (MRM) method was established and performed well in distinguishing different gelatins, particularly in discerning horse-hide gelatin (HHG) and mule-hide gelatin (MHG) from donkey-hide gelatin (DHG). The market investigation revealed the serious adulteration of DHG. Meantime, the pseudo-targeted peptidomics could be used to screen marker peptides of other gelatin foods.

Fingerprint profiling and gut microbiota regulation of polysaccharides from Fritillaria species.

Few studies reported the quality evaluation and gut microbiota regulation effect of polysaccharides from Fritillaria species. In this study, polysaccharides extracted from ten Fritillaria species were compared and distinguished through multi-levels evaluation strategy and data fusion. Furthermore, the gut microbiota regulation effect of polysaccharides among different species was analyzed and evaluated. The fingerprint profiling of IR, molecular weight distribution of polysaccharides, chromatogram of partially hydrolyzed polysaccharides (oligosaccharides) and completely hydrolyzed polysaccharides (monosaccharides) were similar, and no exclusive signals were observed. However, the signal strength of functional group, oligosaccharides abundance and monosaccharides proportion showed obvious differences in inter- and intra-species. Glucan may be the main component of polysaccharides in Fritillaria species, CIRR derived from CIR, PRZ, DEL, TAI, UNI possessed higher total polysaccharides content, polymerization degree, oligosaccharides abundance (DP 2-4), and glucose content than the others. Meanwhile, data fusion model was established for identification of affinis and multi-original species, the accuracy of which proved to be 100 %. In addition, Fritillaria polysaccharides could increase the bacterial community richness and diversity, regulate the gut microbiota composition and possessed potential therapeutic effects on gastrointestinal diseases and nervous system diseases.

The content and distribution of 18 phenolic compounds in 462 batches of edible flowers from 73 species commercially available in China.

Phenolic compounds are widely distributed in plant flowers. The present study systematically analyzed 18 phenolic compounds, represented by 4 monocaffeoylquinic acids, 4 dicaffeoylquinic acids, 5 flavones and 5 other phenolic acids, in 73 species (462 batches of samples) of edible flowers by a new established and validated HPLC-UV (high-performance liquid chromatography ultraviolet) (327/217 nm) method. Among all the species analyzed, 59 species were demonstrated to contain at least one or more quantifiable phenolic compounds, especially in families of Composite, Rosaceae and Caprifoliaceae. 3-Caffeoylquinic acid was found to be the most ubiquitous phenolic compound (in 193 batches of 73 species with the content between 0.061 and 65.10 mg/g), followed by rutin and isoquercitrin. While sinapic acid, 1-Caffeoylquinic acid and 1,3-dicaffeoylquinic acid (only in 5 batches of 1 specie with the content between 0.069 and 0.12 mg/g) were the least ones both in ubiquity and concentration. Additionally, the distribution and abundances of phenolic compounds were compared between these flowers, which would be valuable for auxiliary authentication or other usages. This research covered almost all edible and medicinal flowers in the Chinese market with 18 phenolic compounds therein quantified, which delivered a bird view of phenolic compounds in a broad perspective of edible flowers.

Comparative identification of phytoecdysteroids in Achyranthes bidentata Blume and its three analogous species and application in differentiation between processing products from different species.

The differentiation of raw herbal products from similar species have been achieved by plant metabolomics. However, the distinguishment on various processed products with improved activities and wide clinical utilization from similar species is still tricky due to obscure composition variations during processing. In this study, a comprehensive analysis of phytoecdysteroids in Achyranthes bidentata Blume (AB) and its three analogous species, which were all called Niuxi in Chinese, was conducted on UPLC-HRMS by integrating dynamic exclusion acquisition with data post-processing of targeted multilateral mass defect filter. Two most frequently used species, AB and Cyathula officinalis Kuan (CO) were systematically compared with plant metabolomics methods. And the differential components from the raw materials were evaluated on the ability of distinguishing processed products. The substitution of hydroxyl groups on C-21, C-20, C-22 and C-25 were determined by characteristic mass differences, leading to systematical characterization of 281 phytoecdysteroids. In plant metabolomics studies of raw AB and CO, 16 potential markers were filtered by VIP value > 1, and displayed satisfactory differentiation on the processed AB and CO. The results facilitated the quality control of the four species, especially the processed products of AB and CO, also provided a reference method for the quality control of other processed products.

Comprehensive quality evaluation of Aconiti Lateralis Radix Praeparata based on pseudotargeted metabolomics and simultaneous determination of fifteen components, and development of new processed products of black slices with less toxicity.

Aconiti Lateralis Radix Praeparata is one of the most famous traditional Chinese medicines possessing a variety of pharmacological activities on top of the toxicities. Due to the heterogeneity and non-standardization of the processing procedures, the subtypes and contents of the differential compounds between different processed products still remained indistinct, causing great risk in their proper use. In order to achieve the comparison and quality evaluation of different processed products of Aconiti Lateralis Radix Praeparata and develop new processed products with less toxicity, a quantification and pseudotargeted metabolomics method was developed based on the dynamic MRM mode of triple quadrupole (QqQ) mass spectrometry, and multivariate statistical analysis methods were applied to compare different processed products. Method validation results indicated good specificity, linearity, repeatability, precision, stability and recovery of the established quantification method and good linearity, precision and stability of the pseudotargeted metabolomics method. Differential compounds of different processed products were screened out and further confirmed by the quantification results. At last, the processing procedures were optimized to obtain new processed products of "Heishunpian" (black slices) with less toxicity, in which the contents of the toxic diester-type diterpenoid alkaloids were reduced from 106.98 µg/g to 0.85-12.96 µg/g. This study provided a valuable reference for the establishment of comprehensive quality evaluation methods of herbal medicines and a scientific basis for the optimization of processing procedures of Aconiti Lateralis Radix Praeparata.

Enhanced profiling and quantification of ginsenosides from mountain-cultivated ginseng and comparison with garden-cultivated ginseng.

Panax ginseng can be generally divided into mountain-cultivated ginseng (MCG) and garden-cultivated ginseng (GCG). The market price of MCG is significantly higher than that of GCG. However, the chemical compositions of MCG and the differences from GCG remained unclear. In this study, an integrated strategy combing an offline two-dimensional liquid chromatography separation, LTQ-orbitrap dual mode acquisition, and Q-trap full quantification/quasi-quantification was proposed to explore and compare the chemical compositions of MCG. Consequently, 559 ginsenosides were characterized, among which 437 ginsenosides were in-depth characterized with α-chain and ß-chain annotated. Subsequently, enhanced quantification of 213 ginsenosides was conducted in 57 batches of MCG and GCG. Ginsenosides were found more abundant in MCG than GCG. In addition, 25-year-old MCG could be distinctly differentiated from 15/20-year-old MCG. This strategy facilitated the enhanced profiling and comparison of ginsenosides, improved the quality control tactics of MCG and provided a reference approach for other ginseng related products.

Identification of Pinelliae Rhizoma and its counterfeit species based on enzymatic signature peptides from toxic proteins.

BACKGROUND: Pinelliae Rhizoma (PR), a toxic medication, with long history, is commonly used for eliminating phlegm. Due to the shortage of wild resources and the relative lacking of cultivation technology, it is often confused with its counterfeit species in the market, such as Typhonii Rhizoma (TR), Arisaematis Rhizoma (AR) and tubers of Typhonium flagelliforme (TF) and Pinellia pedatisecta (PP). PURPOSE: It was aimed to screen signature enzymatic peptides from toxic proteins to identify PR and its four counterfeit species. STUDY DESIGN: A comparative proteogenomics strategy based on open-source transcriptome data was applied for screening signature peptides from toxic proteins, which were applied for species authentication of PR and its counterfeit species. METHODS: Firstly, the open-source transcriptome data was used for constructing the annotated protein database, which was used for peptides identification. Secondly, the toxicity of different fractions of PR were evaluated by the rat peritoneal inflammation model. Furthermore, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to profile the main proteins bands of five species, whose sequences were identified based on the in-gel digestion experiment by using ultra-high-performance liquid chromatography/quadrupole-Orbitrap mass spectrometry. Finally, the label-free proteomic analysis was performed to character the proteins and screen the signature peptides of five species, which were validated in commercially available products by dynamic multi reaction monitor (DMRM). RESULTS: The results in this study confirmed that protein was the main toxic components of PR. Both Pinellia ternata agglutinin (PTA) and trypsin inhibitor (TI) like proteins are the main proteins, which were characterized by proteomic analysis based on four annotated protein database. Meanwhile, seven signature peptides from toxic proteins were screened and validated with good repeatability and specificity in commercial products. CONCLUSION: Seven signature enzymatic peptides from toxic protein screened by the comparative proteogenomics strategy based on open-source transcriptome data achieved good identification ability of PR and its four counterfeit species.

Deep chemical identification of phytoecdysteroids in Achyranthes bidentata Blume by UHPLC coupled with linear ion trap-Orbitrap mass spectrometry and targeted isolation.

Achyranthes bidentata Blume is widely used as a traditional Chinese medicine with the effects of nourishing the liver and kidneys and strengthening muscles and bones. In this work, a rapid and simple strategy was developed for characterizing phytoecdysteroids by ultra-high-performance liquid chromatography coupled with liner ion trap-Orbitrap mass spectrometry using electrospray ionization in the negative mode. As a result, 47 phytoecdysteroids were unambiguously or tentatively characterized. Among them, seven known compounds were identified according to the reference standards along with molecular formula, retention time and fragmentation patterns, while others were mostly potential new compounds. Through targeted isolation, the structures of three new compounds were determined by NMR spectra, which were consistent with LC-MS characterization. The present study provides an efficient method to deeply characterize phytoecdysteroids.

Systematic screening and structural characterization of dipeptides using offline 2D LC-LTQ-Orbitrap MS: A case study of Cordyceps sinensis.

Cordyceps sinensis (C. sinensis) is a widely used and highly valuable traditional Chinese medicine. Several dipeptides have been detected in C. sinensis, but current scientific knowledge of its chemical makeup remains limited. In this study, an improved approach that integrates offline two-dimensional liquid chromatography (2D LC) separation, precursor ion list, library screening, and diagnostic ion filtering was established to systematically screen and characterize dipeptides in C. sinensis. Offline 2D LC integrating hydrophilic interaction LC and reverse phase separations was established to eliminate interference and identify the target dipeptides. A library containing the potential 400 dipeptides was created, and a precursor ion list with all theoretical precursor ions was adopted to trigger the MS/MS scan with high sensitivity. To identify dipeptides, the type and connection sequence of amino acids were determined according to the product ions. Ile and Leu residues were differentiated for the first time according to the characteristic ion at m/z 69.07. Ultimately, 170 dipeptides were identified or tentatively characterized from C. sinensis, and most are reported for the first time in this species herein. In addition, the identified dipeptides were also applied for discrimination among the three Cordyceps species, and 11 markers were identified. The obtained results provide a deeper understanding of the chemical basis of C. sinensis.