Biolabel-led research pattern positions the effects and mechanisms of Sophorae Tonkinensis radix et rhizome on lung diseases: A novel strategy for computer-aided herbal medicine research based on omics and bioinformatics

Sophorae tonkinensis radix et rhizoma: A comprehensive review of the ethnopharmacology, phytochemistry, pharmacology, pharmacokinetics, toxicology and detoxification strategy

ETHNOPHARMACOLOGICAL RELEVANCE

Sophorae tonkinensis Radix et Rhizoma (STR), the dried root and rhizome of Sophora tonkinensis Gagnep., is commonly used in the treatment of tonsillitis and pharyngitis, throat soreness and throat obstruction, swelling and aching of gum, etc. in China or other Asian countries. STR is usually used as the core herb in traditional Chinese medicine preparations, such as "Biyanling Tablets", "Fufang Muji Granules" and "Ganyanling Injections", etc. AIM OF THE REVIEW: This review aimed to provide a comprehensive analysis of STR in terms of botany, traditional use, phytochemistry, ethnopharmacology, pharmacology, pharmacokinetics, toxicology and detoxification strategy, to provide a rational application in future research.

MATERIALS AND METHODS

The information involved in the study was gathered from a variety of electronic resources, including China National Knowledge Infrastructure (CNKI), SciFinder, Google Scholar, PubMed, Web of Science, and Chinese Masters and Doctoral Dissertations.

RESULTS

Till now, a total of 333 chemical components have been identified in STR, including 85 alkaloids, 124 flavonoids, 24 triterpenes, 27 triterpene saponins, 34 organic acids, 8 polysaccharides, etc. STR and its main active constituents have cardiovascular protection, anti-tumor activity, anti-inflammatory activity, antipyretic activity, analgesic activity, antibacterial activity, antifungal activity, antiviral activity, and hepatoprotective activity, etc. However, toxic effects of STR on the liver, nerves, heart, and gastrointestinal tract have also been observed. To mitigate these risks, STR needs attenuation before use, with the most common detoxification methods being processing and combined use with other drugs. The pharmacokinetics of STR in vivo and traditional and clinical prescriptions containing STR have been sorted out. Despite the potential therapeutic benefits of STR, further research is warranted to elucidate its hepatotoxicity, particularly in vivo, exploring aspects such as in vivo metabolism, distribution, and mechanisms.

CONCLUSION

This review serves to emphasize the therapeutic potential of STR and highlights the crucial need to address its toxicity concerns before considering clinical application. Further research is required to comprehensively investigate the toxicological properties of STR, with particular emphasis on its hepatotoxicity and neurotoxicity. Such research endeavors have the potential to standardize the rational application of STR for optimal therapeutic outcomes.

Combination of omics, bioinformatics, molecular docking, and experimental validation to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen

Omics, bioinformatics, molecular docking, and experimental validation were used to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen (SDG) based on the biolabel-led research pattern. Integrated omics were used to explore the biolabels of SDG intervention in liver tissue. Subsequently, bioinformatics and molecular docking were applied to topologically analyze its therapeutic effects, mechanisms, and active compounds based on biolabels. Finally, an animal model was used to verify the biolabel analysis results. Omics, bioinformatics, and molecular docking revealed that SDG may exert therapeutic effects on liver diseases in the multicompound and multitarget synergistic modes, especially liver cirrhosis. In the validation experiment, SDG and its active compounds (betulinic acid and gallic acid) significantly improved the liver histopathological damage in the CCl4-induced liver cirrhosis model. Meanwhile, they also produced significant inhibitory effects on the focal adhesion pathway (integrin alpha-1, myosin regulatory light chain 2, laminin subunit gamma-1, etc.) and alleviated the associated pathological processes: focal adhesion (focal adhesion kinase 1)-extracellular matrix (collagen alpha-1(IV) chain, collagen alpha-1(VI) chain, and collagen alpha-2(VI) chain) dysfunction, carcinogenesis (alpha-fetoprotein, NH3, and acetylcholinesterase), inflammation (tumor necrosis factor alpha, interleukin-1 [IL-1], IL-6, and IL-10), and oxidative stress (reactive oxygen species, malonaldehyde, and superoxide dismutase). This study provides new evidence and insights for the hepatoprotective effects, mechanisms, and active compounds of SDG.

Liver protein and metabolite biolabels reveal hepatoprotective effects and active compounds of Eucommiae folium: Exploration of new application of herb based on multi-omics and bioinformatics

A biolabel-led research based on multi-omics and bioinformatics was applied to analyze the application value of Eucommiae folium (EF) in liver cirrhosis, as well as the mechanism of action and material basis. Multi-omics were used to analyze the biolabels and key pathways of EF intervention in liver tissue. Subsequently, based on the information, bioinformatics was used to analyze the application value of EF in liver disease, as well the mechanism of action and material basis. Finally, histopathological and target expression analyses in an animal model were used to verify biolabels analysis results. Multi-omics showed that 18 proteins and 10 metabolites involved in five key pathways were screened as biolabels. Bioinformatics suggested that the application value of EF for liver cirrhosis may be the highest among the liver diseases that it may treat. Additionally, EF and five active compounds (curcumol, eucalyptol, (+)-catechin, naringenin, and quercetin) may protect the cirrhotic liver against the excessive energy expenditure and hepatic stellate cells activation through suppressing the oxidative phosphorylation pathway in a CCl4-induced mouse model. This study provides reference and evidence for the application value of EF in liver diseases, especially liver cirrhosis.

Sophora tonkinensis and active compounds inhibit mitochondrial impairments, inflammation, and LDLR deficiency in myocardial ischemia mice through regulating the vesicle-mediated transport pathway

Ancient Chinese medicine literature and modern pharmacological studies show that Sophora tonkinensis Gagnep. (ST) has a protective effect on the heart. A biolabel research based on omics and bioinformatics and experimental validation were used to explore the application value of ST in the treatment of heart diseases. Therapeutic potential, mechanism of action, and material basis of ST in treating heart diseases were analyzed by proteomics, metabolomics, bioinformatics, and molecular docking. Cardioprotective effects and mechanisms of ST and active compounds were verified by echocardiography, HE and Masson staining, biochemical analysis, and ELISA in the isoproterenol hydrochloride-induced myocardial ischemia (MI) mice model. The biolabel research suggested that the therapeutic potential of ST for MI may be particularly significant among the heart diseases it may treat. In the isoprenaline hydrochloride-induced MI mice model, ST and its five active compounds (caffeic acid, gallic acid, betulinic acid, esculetin, and cinnamic acid) showed significant protective effects against echocardiographic changes and histopathological damages of the ischemic myocardial tissue. Meanwhile, they showed a tendency to correct mitochondrial structure and function damage and the abnormal expression of 12 biolables (DCTN1, DCTN3, and SCARB2, etc.) in the vesicle-mediated transport pathway, inflammatory cytokines (IL-1β, IL-6, and IL-10, etc.), and low density lipoprotein receptor (LDLR). The biolabel research identifies a new application value of ST in the treatment of heart diseases. ST and its active compounds inhibit mitochondrial impairments, inflammation, and LDLR deficiency through regulating the vesicle-mediated transport pathway, thus achieving the purpose of treating MI.

iTRAQ-Based Proteomic and Physiological Analyses Reveal the Mechanisms of Dehydration and Cryopreservation Tolerance of Sophora tonkinensis Gagnep. Seeds

Sophora tonkinensi is a shrub of the genus Sophora in the family Fabaceae with anti-inflammatory and pain-relieving effects. While the cultivation, chemical makeup, and medicinal properties of S. tonkinensis have been reported, the physiological mechanisms governing its dehydration and cryopreservation tolerance of seeds remain unclear. In this study, we investigated the morphological, physiological, biochemical, and protein expression characteristics of S. tonkinensis seeds subjected to dehydration and cryopreservation techniques via the observation of cell microstructure, determination of antioxidant enzyme activity, and iTRAQ-based proteomic analysis, respectively. The results of the study demonstrated that the seeds possessed a certain level of tolerance to dehydration. The highest germination percentage of 83.0% was observed after 2 h of dehydration (10.1% water content), which was identified as the optimal time point for cryopreservation. However, the germination percentage was reduced to only 30.5% when the water content reached 5.4%, indicating that S. tonkinensis seeds exhibit intermediate storage behavior. Further investigation revealed that during seed dehydration and cryopreservation treatment, liposomes were gradually and highly fused, whereas the activities of ROS scavenging and stress defense were significantly enhanced. During dehydration, the seed tissues formed a protective mechanism of stress resistance based on protein processing in the endoplasmic reticulum and antioxidant system, which was related to the dehydration tolerance. Moreover, only three differentially expressed LEA proteins were identified, and it is speculated that the strengthening of intracellular metabolism and the absence of specific LEA and dehydrins could be crucial factors for the reduced germination percentage after excessive dehydration and cryopreservation.

Eucommiae Folium and Active Compounds Protect Against Mitochondrial Dysfunction-Calcium Overload in Epileptic Hippocampal Neurons Through the Hypertrophic Cardiomyopathy Pathway

Epilepsy is a chronic brain disease and often occurs suddenly for no reason. Eucommiae folium (EF), an edible herb, can be used in the treatment of various kinds of brain diseases in clinic. From the perspective of safety and efficacy, EF is especially suitable for the treatment of chronic brain diseases. With the help of biolabels, this study was aimed to explore the value and feasibility of EF in the treatment of epilepsy. Proteomics and metabolomics were used to explore the biolabels of EF intervention in brain tissues. Bioinformatics was then applied to topologically analyze its neuroprotective effects and mechanisms and material basis based on biolabels, which were validated in an animal model. The biolabel-led research revealed that EF may exert the therapeutic potential to treat brain diseases through the interaction between multiple compounds and multiple targets, among which its therapeutic potential for epilepsy is particularly prominent. In the pentylenetetrazole-induction model, EF and four active compounds (oleamide, catechol, chlorogenic acid, and kaempferol) protected epileptic hippocampal neurons (Nissl and FJB staining) against mitochondrial dysfunction (MYH6, MYL3, and MYBPC3, etc.) and calcium overload (TNNI3, TNNC1, and TNNT2, etc.) through the hypertrophic cardiomyopathy pathway. This study provides new evidence and insights for the neuroprotective effects of EF, in which four active compounds may be potential drug candidates for the treatment of epilepsy.

Omics combined with network pharmacology reveal the neuroprotective mechanism of Sophora tonkinensis based on the biolabel research pattern: The treatment of Parkinson's disease against oxidative stress and neuroexcitatory toxicity

Based on the biolabel research pattern, omics and network pharmacology were used for exploring the neuroprotection of Sophora tonkinensis (ST) in the treatment of brain diseases. Multi-omics were applied to investigate biolabels for ST intervention in brain tissue. Based on biolabels, the therapeutic potential, mechanism and material basis of ST for treating brain diseases were topologically analyzed by network pharmacology. A Parkinson's disease (PD) mouse model was used to validate biolabel analysis results. Four proteins and three metabolites were involved in two key pathways (alanine, aspartate and glutamate metabolism and arginine biosynthesis) and considered as biolabels. Network pharmacology showed that ST has the potential to treat some brain diseases, especially PD. Eight compounds (including caffeic acid, gallic acid and cinnamic acid) may serve as the material basis of ST treating brain diseases via the mediation of three biolabels. In the PD model, ST and its active compounds (caffeic acid and gallic acid) may protect dopaminergic neurons (maximum recovery rate for dopamine, 49.5%) from oxidative stress (E3 ubiquitin-protein ligase parkin, reactive oxygen species, nitric oxide, etc.) and neuroexcitatory toxicity (glutamate dehydrogenase, glutamine, glutamic acid, etc.). These findings indicated that omics and network pharmacology may contribute to the achievement of the objectives of this study based on the biolabel research pattern.

POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability

Mass spectrometry-based proteomic technique has become indispensable in current exploration of complex and dynamic biological processes. Instrument development has largely ensured the effective production of proteomic data, which necessitates commensurate advances in statistical framework to discover the optimal proteomic signature. Current framework mainly emphasizes the generalizability of the identified signature in predicting the independent data but neglects the reproducibility among signatures identified from independently repeated trials on different sub-dataset. These problems seriously restricted the wide application of the proteomic technique in molecular biology and other related directions. Thus, it is crucial to enable the generalizable and reproducible discovery of the proteomic signature with the subsequent indication of phenotype association. However, no such tool has been developed and available yet. Herein, an online tool, POSREG, was therefore constructed to identify the optimal signature for a set of proteomic data. It works by (i) identifying the proteomic signature of good reproducibility and aggregating them to ensemble feature ranking by ensemble learning, (ii) assessing the generalizability of ensemble feature ranking to acquire the optimal signature and (iii) indicating the phenotype association of discovered signature. POSREG is unique in its capacity of discovering the proteomic signature by simultaneously optimizing its reproducibility and generalizability. It is now accessible free of charge without any registration or login requirement at https://idrblab.org/posreg/.