Stepwise targeted matching strategy from in vitro to in vivo based on ultra-high performance liquid chromatography tandem mass spectrometry technology to quickly identify and screen pharmacodynamic constituents

A Q-marker screening strategy based on ADME studies and systems biology for Chinese herbal medicine, taking Qianghuo Shengshi decoction in treating rheumatoid arthritis as an example

Chinese herbal medicine (CHM) exhibits a broad spectrum of clinical applications and demonstrates favorable therapeutic efficacy. Nonetheless, elucidating the underlying mechanism of action (MOA) of CHM in disease treatment remains a formidable task due to its inherent characteristics of multi-level, multi-linked, and multi-dimensional non-linear synergistic actions. In recent years, the concept of a Quality marker (Q-marker) proposed by Liu et al. has significantly contributed to the monitoring and evaluation of CHM products, thereby fostering the advancement of CHM research. Within this study, a Q-marker screening strategy for CHM formulas has been introduced, particularly emphasising efficacy and biological activities, integrating absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification. As an illustrative case, the Q-marker screening of Qianghuo Shengshi decoction (QHSSD) for treating rheumatoid arthritis (RA) has been conducted. Consequently, from a pool of 159 compounds within QHSSD, five Q-markers exhibiting significant in vitro anti-inflammatory effects have been identified. These Q-markers encompass notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Furthermore, by employing an integrated analysis of network pharmacology and metabolomics, several instructive insights into pharmacological mechanisms have been gleaned. This includes the identification of key targets and pathways through which QHSSD exerts its crucial roles in the treatment of RA. Notably, the inhibitory effect of QHSSD on AKT1 and MAPK3 activation has been validated through western blot analysis, underscoring its potential to mitigate RA-related inflammatory responses. In summary, this research demonstrates the proposed strategy's feasibility and provides a practical reference model for the systematic investigation of CHM formulas.

A strategy to explore the quality markers of Ziziphi Spinosae semen by combining metabolic in vivo study with network pharmacology

Ziziphi Spinosae semen (ZSS), the dried and ripe seed of Ziziphus jujube Mill. var. spinosa (Bunge) Hu ex H. F. Chou, has been used as a sedative in China and other Asian countries for over a millennium. However, its quality markers (Q-markers) are not completely clear. In this study, Q-markers selected by a metabolic in vivo study combined with network pharmacology are proposed for ZSS quality control. An UHPLC (ultra-high-performance liquid chromatography)-Q-Orbitrap-MS method was developed to identify or tentatively assign 48 components including 21 flavonoid C-glycosides, 2 flavonoid O-glycosides, 11 dammarane triterpenoid saponins, 13 alkaloids, and 1 other, using a diagnostic product ion filtering strategy in ZSS. Subsequently, 147 metabolites detected from serum, urine, bile, and feces samples of para-chlorophenylalanine-induced insomnia rats treated with ZSS aqueous extracts could be linked to their respective parent compounds, including 27 prototypes. Meanwhile, three metabolic networks of flavonoids, saponins, and alkaloids are preliminarily established and potential metabolic pathways are investigated under the insomnia condition. Finally, 12 key bioactive components against insomnia including magnoflorine, caaverine, coclaurine, norisocorydine, genkwanin, juzinrine, apigenin, jujubogenin, kaempferol-3-O-rutinoside, jujuboside A, jujuboside B, and spinosin with the highest degree values in component-target-pathways network were selected as Q-markers for the quality control of ZSS.

Integrated Strategy From In Vitro, In Situ, In Vivo to In Silico for Predicting Active Constituents and Exploring Molecular Mechanisms of Tongfengding Capsule for Treating Gout by Inhibiting Inflammatory Responses

The study of screening active constituents from traditional Chinese medicine (TCM) is important for explicating the mechanism of action of TCM and further evaluating the safety and efficacy effectively. However, detecting and identifying the active constituents from complicated biological samples still remain a challenge. Here, a practical, quick, and novel integrated strategy from in vitro, in situ, in vivo to in silico for rapidly screening the active constituents was developed. Firstly, the chemical profile of TCM in vitro was identified using UPLC-Q Exactive-Orbitrap HRMS. Secondly, the in situ intestinal perfusion with venous sampling (IPVS) method was used to investigate the intestinal absorption components. Thirdly, after intragastric administration of the TCM extract, the in vivo absorbed prototype components were detected and identified. Finally, the target network pharmacology approach was applied to explore the potential targets and possible mechanisms of the absorbed components from TCM. The reliability and availability of this approach was demonstrated using Tongfengding capsule (TFDC) as an example of herbal medicine. A total of 141 compounds were detected and identified in TFDC, and among them, 64 components were absorbed into the plasma. Then, a total of 35 absorbed bioactive components and 50 related targets shared commonly by compounds and gout were integrated via target network pharmacology analysis. Ultimately, the effects of the absorbed components on metabolism pathways were verified by experiments. These results demonstrated that this original method may provide a practical tool for screening bioactive compounds from TCM treating particular diseases. Furthermore, it also can clarify the potential mechanism of action of TCM and rationalize the application of TFDC as an effective herbal therapy for gout.

Research on the effect of spleen-invigorating and anti-swelling active ingredients in crude and processed coix seed based on Spectrum - Effects relationship combined with chemometrics

Coix seed (CS) is the dry mature seed kernel of Coix lacrma-jobi L. var. mayuen (Roman.) Stapf, which has the effect of spleen-invigorating and anti-swelling. However, research reports on the main active ingredients of CS were minimal. The purpose of this study was to find the main active ingredients that affect the efficacy of CS to invigorate the spleen and reduce swelling through the spectrum-effect relationship, combined with chemometrics, grey relational analysis (GRA) and entropy method, and to compare the differences between the effects of crude and processed CS. First of all, the HPLC-ELSD method was used to establish the chromatographic fingerprint of CS, and 12 batches of CS samples were analyzed through chemometrics in this study. Then, we studied the effect of spleen-invigorating and anti-swelling in CS. Finally, through grey relational analysis and entropy method, the spectrum-effect relationship between the chromatographic fingerprint and the seven pharmacodynamic effect indexes was studied. The results showed that the main pharmacologically active ingredients were 1,3-Dioleoyl-2-palmitoylglycerol (peak 8), 1,2-dilinoleoyl-3-oleoyl-rac-glycerol (peak 2), 1,3-Dipalmitoyl-2-Linolein (peak 5), 1,2-Dilinoleoyl-3-palmitoyl-rac-glycerol (peak 3), 1,2-Dioleoyl-3-linoleoyl-rac-glycerol (peak 4), and glycerol trioleate (peak 7), and the comprehensive efficacy of bran-fried CS was better than that of raw CS. In summary, we have identified the main active ingredients related to the efficacy of CS. As far as we know, this is the first time that the crude and processed CS spectrum-effect relationship has been established and compared, which provides a theoretical basis for subsequent studies on the material basis and molecular mechanism of CS pharmacodynamics.

Mechanism of Paeoniae Radix Alba in the Treatment of Non-alcoholic Fatty Liver Disease Based on Sequential Metabolites Identification Approach, Network Pharmacology, and Binding Affinity Measurement

Screening functional food ingredients (FFI) from medicinal and edible plants (MEP) has still remained a great challenge due to the complexity of MEP and its obscure function mechanisms. Herein, an integrated strategy based on sequential metabolites identification approach, network pharmacology, molecular docking, and surface plasmon resonance (SPR) analysis was proposed for quickly identifying the active constituents in MEP. First, the sequential biotransformation process of MEP, including intestinal absorption and metabolism, and hepatic metabolism, was investigated by oral gavage, and intestinal perfusion with venous sampling method. Then the blood samples were analyzed by UPLC-Q Exactive Orbitrap HRMS. Second, the network pharmacology approach was used to explore the potential targets and possible mechanisms of the in vivo metabolites of MEP. Third, molecular docking and SPR approaches were used to verify the specific interactions between protein targets and representative ingredients. The proposed integrated strategy was successfully used to explore the heptoprotective components and the underlying molecular mechanism of Paeoniae Radix Alba (PRA). A total of 44 compounds were identified in blood samples, including 17 porotypes and 27 metabolites. The associated metabolic pathways were oxidation, methylation, sulfation, and glucuronidation. After further screening, 31 bioactive candidates and 377 related targets were obtained. In addition, the bioactive components contained in PRA may have therapeutic potentials for non-alcoholic fatty liver disease (NAFLD). The above results demonstrated the proposed strategy may provide a feasible tool for screening FFI and elaborating the complex function mechanisms of MEP.

Poria cocos could ameliorate cognitive dysfunction in APP/PS1 mice by restoring imbalance of Aβ production and clearance and gut microbiota dysbiosis

Alzheimer's disease (AD) is the most common neurodegenerative disorder. Amyloid beta-protein (Aβ) plaques, which are the hallmark of AD, are formed from the imbalance of Aβ production and clearance accompanied by neuroinflammation, gut dysbiosis, and metabolite dysfunction. All of these processes give rise to neurochemical deficiencies and synaptic dysfunction, which ultimately contribute to recognition dysfunction. Poria cocos (PC), which contains multiple active ingredients, plays a significant role in the treatment of multiple-pathogenesis senile diseases such as AD. Nevertheless, there are only very few investigations on the intricate action mechanism of PC for the treatment of AD. In this study, we evaluate the multi-target cure effect of PC on APP/PS1 mice by behavioral, immunohistochemical (IHC), targeted metabolomics, and 16S rRNA sequencing experiments. Mice treated with PC showed significant improvements in cognitive function as evaluated by the behavioral experiment. IHC revealed that PC treatment relieved Aβ deposition by reducing the formation of Aβ and increasing its clearance. Moreover, PC treatment improved gut dysbiosis, which reversed the metabolite dysfunction of bile acid. These findings reveal that PC is a promising therapeutic agent, which might ameliorate the cognitive function of AD by restoring the imbalance of Aβ production and clearance and gut microbiota dysbiosis.

Comparative pharmacokinetics of Ding-Zhi-Xiao-Wan preparation and its single herbs in rats by using a putative multiple-reaction monitoring UPLC-MS/MS method

INTRODUCTION

The formula of Chinese medicine, Ding-Zhi-Xiao-Wan (DZXW), has the distinct feature of compatibility therapy, which is attributed to the interactions of multi-herbs. However, the quantification problem caused by the absence of pure reference standards is a bottleneck to clarify the compatibility advantages from the perspective of pharmacokinetics (PKs).

OBJECTIVE

This study aimed to develop a putative multiple-reaction monitor (PMRM) strategy for exploring the comparative PKs of DZXW and its single herbs.

METHODS

First, precursor ion and tandem mass spectrometry (MS/MS) chromatograms were obtained via ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight MS (UHPLC-Q-TOF-MS) under different collision energy (CE) values. Then, the two most abundance ions in the MS/MS chromatograms were chosen as product ions, and CE values were selected according to the abundance of the product ion peaks. Next, a PMRM strategy consisting of optimal MRM parameters was constructed. Finally, the established PMRM parameters were imported to UHPLC coupled with triple quadrupole MS (UHPLC-TQ-MS) for quantification.

RESULTS

The strategy was exemplified by the comparative PK study of DZXW and its single herbs. This strategy could extend the PK scopes of multi-components. The quantitative results displayed substantial variations in PK parameters between DZXW and its single herbs.

CONCLUSION

The PK parameters indicated that the DZXW formula could increase the exposure levels of most ingredients and reduce the maximum concentration (C_max ) of Radix Polygala, indicating that herb compatibility could produce synergistic effects and diminish possible toxic effects. This study provides a viable orientation for the compatibility investigation of traditional Chinese medicine.

Exploring the Active Components of Simotang Oral Liquid and Their Potential Mechanism of Action on Gastrointestinal Disorders by Integrating Ultrahigh-Pressure Liquid Chromatography Coupled with Linear Ion Trap-Orbitrap Analysis and Network Pharmacology

Simotang oral liquid (SMT), a well-known traditional Chinese medicine formula composed of four medicinal and edible plants, has been extensively used for treating gastrointestinal disorders (GIDs) since ancient times. However, the major active constituents and the underlying molecular mechanism of SMT on GIDs are still partially understood. Herein, the preliminary chemical profile of SMT was first identified by ultrahigh-pressure liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap). In total, 70 components were identified. Then, a network pharmacology approach integrating target prediction, pathway enrichment analysis, and network construction was adopted to explore the therapeutic mechanism of SMT. As a result, 170 main targets were screened out and considered as effective players in ameliorating GIDs. More importantly, the major hubs were found to be highly enriched in a calcium signaling pathway. Furthermore, 26 core SMT-related genes were identified, which may play key roles in ameliorating gastrointestinal motility. In conclusion, this work would provide valuable information for further development and clinical application of SMT.

Stepwise rapid tracking strategy to identify active molecules from Ixeris sonchifolia Hance based on "'affinity mass spectrometry-atomic force microscopy imaging'" technology

In this study, a novel stepwise rapid tracking strategy was reported to identify the active molecules from Ixeris sonchifolia Hance (IsH) in the treatment of coronary heart disease (CHD) based on "affinity mass spectrometry (MS)-atomic force microscopy (AFM) imaging" technology. First, vascular endothelial growth factor receptor 2 (VEGFR2) of the vascular endothelial growth factor (VEGF) signal transduction pathway located on the cell membrane was revealed to be the core target protein in CHD treatment through network pharmacology and bioinformatics. In addition, affinity MS screening based on VEGFR2 identified isochlorogenic acid A and luteolin-7-O-glucuronide as having stronger affinity with VEGFR2. Then, the active molecule was elucidated based on the observation that its actions accompanied the molecular morphological changes by AFM imaging and it could act on the binding pocket of VEGFR2 through molecular docking which further demonstrated the analysis and inference of AFM imaging. The methyl thiazolyl tetrazolium (MTT) assay finally confirmed that the active molecules specifically combined with the potential core target protein to protect the viability of cardiomyocytes, which identified the main potential active molecules in IsH for the treatment of CHD and provided a possible mechanism for the protective role of the drug. The technology established in this study could facilitate the rapid tracing of potential active molecules in traditional Chinese medicine (TCM), which would provide further a reference for research on quality, molecular mechanisms and new drugs.

Corydalis Rhizoma as a model for herb-derived trace metabolites exploration: A cross-mapping strategy involving multiple doses and samples

Deciphering the metabolites of multiple components in herbal medicine has far-reaching significance for revealing pharmacodynamic ingredients. However, most chemical components of herbal medicine are secondary metabolites with low content whose in vivo metabolites are close to trace amounts, making it difficult to achieve comprehensive detection and identification. In this paper, an efficient strategy was proposed: herb-derived metabolites were predicted according to the structural characteristics and metabolic reactions of chemical constituents in Corydalis Rhizoma and chemical structure screening tables for metabolites were conducted. The fragmentation patterns were summarized from representative standards combining with specific cleavage behaviors to deduce structures of metabolites. Ion abundance plays an important role in compound identification, and high ion abundance can improve identification accuracy. The types of metabolites in different biological samples were very similar, but their ion abundance might be different. Therefore, for trace metabolites in biological samples, we used the following two methods to process: metabolites of high dose herbal extract were analyzed to characterize those of clinical dose herbal extracts in the same biological samples; cross-mapping of different biological samples was applied to identify trace metabolites based on the fact that a metabolite has different ion abundance in different biological samples. Compared with not using this strategy, 44 more metabolites of clinical dose herbal extract were detected. This study improved the depth, breadth, and accuracy of current methods for herb-derived metabolites characterization.

Discovering the Major Antitussive, Expectorant, and Anti-Inflammatory Bioactive Constituents in Tussilago Farfara L. Based on the Spectrum-Effect Relationship Combined with Chemometrics

Farfarae Flos (FF) is the dried flower bud of Tussilago farfara L, which has antitussive, expectorant, and anti-inflammatory effects. However, little research on the main active composition of FF has been reported. The purpose of this study is to find the main active compounds responsible for the three pharmacological effects (i.e., antitussive, expectorant, and anti-inflammatory effects) of Farfarae Flos, based on the spectrum–effect relationship combined with chemometrics. First, this study uses the UPLC-QDA method to establish the chromatography fingerprint of Farfarae Flos, which is combined with chemometrics to analyze 18 batches of samples. Then, we study the antitussive, expectorant, and anti-inflammatory effects of Farfarae Flos. Finally, the spectrum–effect relationship between the fingerprint and the three pharmacological effects are studied by grey correlation analysis and partial least squares regression. The results show that four, four, and three main active constituents were found for the antitussive, expectorant, and anti-inflammatory pharmacological effects, respectively. In conclusion, we found the main active compounds corresponding to the main pharmacodynamic effects of Farfarae Flos. To our knowledge, this is the first time that spectrum–effect relationships in FF have been established using both raw and processed samples, which provides an experimental basis for further studies on the pharmacodynamic material basis of Farfarae Flos, as well as providing reference for the comprehensive evaluation of Farfarae Flos quality and the development of substitute resources.

An Integrated Approach to Characterize Intestinal Metabolites of Four Phenylethanoid Glycosides and Intestinal Microbe-Mediated Antioxidant Activity Evaluation In Vitro Using UHPLC-Q-Exactive High-Resolution Mass Spectrometry and a 1,1-Diphenyl-2-picrylhydrazyl-Based Assay

Intestinal bacteria have a significant role in metabolism and the pharmacologic actions of traditional Chinese medicine active ingredients. Phenylethanoid glycosides (PhGs), as typical phenolic natural products, possess wide bioactivities, but low oral bioavailability. The aim of this work was to elucidate the metabolic mechanism underlying PhGs in the intestinal tract and screen for more active metabolites. In this study, a rapid and reliable method using an effective post-acquisition approach based on advanced ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid Quadrupole-Orbitrap high resolution mass spectrometry (Q-Exactive-HRMS) provided full MS and HCD MS² data. Thermo Scientific™ Compound Discoverer™ software with a Fragment Ion Search (FISh) function in one single workflow was developed to investigate the intestinal microbial metabolism of four typical PhGs. Furthermore, antioxidant activity evaluation of PhGs and their related metabolites was simultaneously carried out in combination with a 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay to understand how intestinal microbiota transformations modulate biological activity and explore structure–activity relationships (SARs). As a result, 26 metabolites of poliumoside, 42 metabolites of echinacoside, 42 metabolites of tubuloside, and 46 metabolites of 2′-acetylacteoside were identified. Degradation, reduction, hydroxylation, acetylation, hydration, methylation, and sulfate conjugation were the major metabolic pathways of PhGs. Furthermore, the degraded metabolites with better bioavailability had potent antioxidant activity that could be attributed to the phenolic hydroxyl groups. These findings may enhance our understanding of the metabolism, pharmacologic actions, and real active forms of PhGs.