Application of Molecular Methods in the Identification of Ingredients in Chinese Herbal Medicines

Utilization of the Shensheng-Piwen changed medicinal powder extracts combines metal-organic frameworks as an antibacterial agent

Introduction

Widespread opportunistic pathogens pose a serious threat to global health, particularly in susceptible hospital populations. The escalating crisis of antibiotic resistance highlights the urgent need for novel antibacterial agents and alternative treatment approaches. Traditional Chinese Medicine (TCM) and its compounds have deep roots in the treatment of infectious diseases. It has a variety of active ingredients and multi-target properties, opening up new avenues for the discovery and development of antimicrobial drugs.

Methods

This study focuses on assessing the efficacy of the Shensheng-Piwen changed medicinal powder (SPC) extracts against opportunistic pathogen infections by broth microdilution and agar disc diffusion methods. Additionally, biofilm inhibition and eradication assays were performed to evaluate the antibiofilm effects of SPC extracts.

Results

Metabolite profiles were analyzed by LC-MS. Furthermore, the potential synergistic effect between SPC and Metal-Organic Framework (MOF) was investigated by bacterial growth curve analysis. The results indicated that the SPC extracts exhibited antibacterial activity against S. aureus, with a minimum inhibitory concentration (MIC) of 7.8 mg/mL (crude drug concentration). Notably, at 1/2 MIC, the SPC extracts significantly inhibited biofilm formation, with over 80% inhibition, which was critical in tackling chronic and hospital-acquired infections. Metabolomic analysis of S. aureus revealed that SPC extracts induced a notable reduction in the levels of various metabolites, including L-proline, L-asparagine. This suggested that the SPC extracts could interfere with the metabolism of S. aureus. Meanwhile, the growth curve experiment proved that SPC extracts and MOFs had a synergistic antibacterial effect.

Discussion

In conclusion, the present study highlights the potential of SPC extracts as a novel antibacterial agent against S. aureus infections, with promising biofilm inhibition properties. The observed synergistic effect between SPC extracts and MOFs further supports the exploration of this combination as an alternative treatment approach.

Rapid identification of medicinal plants via visual feature-based deep learning

BACKGROUND

Traditional Chinese Medicinal Plants (CMPs) hold a significant and core status for the healthcare system and cultural heritage in China. It has been practiced and refined with a history of exceeding thousands of years for health-protective affection and clinical treatment in China. It plays an indispensable role in the traditional health landscape and modern medical care. It is important to accurately identify CMPs for avoiding the affected clinical safety and medication efficacy by the different processed conditions and cultivation environment confusion.

RESULTS

In this study, we utilize a self-developed device to obtain high-resolution data. Furthermore, we constructed a visual multi-varieties CMPs image dataset. Firstly, a random local data enhancement preprocessing method is proposed to enrich the feature representation for imbalanced data by random cropping and random shadowing. Then, a novel hybrid supervised pre-training network is proposed to expand the integration of global features within Masked Autoencoders (MAE) by incorporating a parallel classification branch. It can effectively enhance the feature capture capabilities by integrating global features and local details. Besides, the newly designed losses are proposed to strengthen the training efficiency and improve the learning capacity, based on reconstruction loss and classification loss.

CONCLUSIONS

Extensive experiments are performed on our dataset as well as the public dataset. Experimental results demonstrate that our method achieves the best performance among the state-of-the-art methods, highlighting the advantages of efficient implementation of plant technology and having good prospects for real-world applications.

Improving the geographical origin classification of Radix glycyrrhizae (licorice) through hyperspectral imaging assisted by U-Net fine structure recognition

Radix glycyrrhizae (licorice) is extensively employed in traditional Chinese medicine, and serves as a crucial raw material in industries such as food and cosmetics. The quality of licorice from different origins varies greatly, so classification of its geographical origin is particularly important. This study proposes a technique for fine structure recognition and segmentation of hyperspectral images of licorice using deep learning U-Net neural networks to segment the tissue structure patterns (phloem, xylem, and pith). Firstly, the three partitions were separately labeled using the Labelme tool, which was utilized to train the U-Net model. Secondly, the obtained optimal U-Net model was applied to predict three partitions of all samples. Lastly, various machine learning models (LDA, SVM, and PLS-DA) were trained based on segmented hyperspectral data. In addition, a threshold method and a circumcircle method were applied to segment licorice hyperspectral images for comparison. The results revealed that compared with the threshold segmentation method (which yielded SVM classifier accuracies of 99.17%, 91.15%, and 92.50% on the training set, validation set, and test set, respectively), the U-Net segmentation method significantly enhanced the accuracy of origin classification (99.06%, 94.72% and 96.07%). Conversely, the circumcircle segmentation method did not effectively improve the accuracy of origin classification (99.65%, 91.16% and 92.13%). By integrating Raman imaging of licorice, it can be inferred that the U-Net model, designed for region segmentation based on the inherent tissue structure of licorice, can effectively improve the accuracy origin classification, which has positive significance in the development of intelligence and information technology of Chinese medicine quality control.

Qiangguyin inhibited fat accumulation in OVX mice through the p38 MAPK signaling pathway to achieve anti-osteoporosis effects

Postmenopausal osteoporosis (PMOP) is a common bone disease characterized by decreased bone density and increased bone fragility due to decreased estrogen levels. Qiangguyin (QGY) is transformed from the famous traditional Chinese medicine BuShen Invigorating Blood Decoction. In this study, we used QGY to treat PMOP. We observed that QGY significantly reduced fat accumulation in the chondro-osseous junction. However, its specific mechanism of action remains unclear. To determine the specific molecular mechanism of QGY, we explored the pharmacological mechanism by which QGY reduces fat accumulation in the chondro-osseous junction through network pharmacological analysis. The active components and targets related to PMOP and QGY were screened from different databases, forming a composition-target-disease network. Next, a comprehensive analysis platform including protein-protein interaction (PPI) network, Gene Ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were established. The results revealed that QGY inhibits adipogenic differentiation by activating the mitogen-activated protein kinase (MAPK) signaling pathway, thus reducing the accumulation of fat in the chondro-osseous junction. For further verification. In vitro and in vivo experiments were carried out. Our data showed that QGY significantly reversed the high expression of fatty acid binding protein 4 (FABP4) and peroxisome proliferator-activated receptor γ (PPARγ). Further, QGY prevents fat accumulation by inhibiting the expression of p38. In summary, the results of this study suggested that QGY-induced phenotypic changes are related to the activation of the p38 MAPK signaling pathway.

Quality assessment of African herbal medicine: A systematic review and the way forward

BACKGROUND

In Africa, herbalism supplements allopathic medicine's efforts to ensure Universal Health Coverage attainment. This review was conducted to identify and to summarise current literature on methodological approaches used for quality control of herbal medicines in Africa, to evaluate the gaps associated with existing strategies within context of best practices, and make recommendations for future improvements.

METHODS

A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Articles were screened and assessed for eligibility.

RESULTS

118 articles were included into the study. There was a high preference for impurity profiling tests (77%) indicating the prioritization for tests that guarantee safety despite the limited analytical resources available. Other classes of tests reported included identification tests (29%), physicochemical tests (18%), and content assays (12%). Although standard methods exist in preparing samples for impurity tests, different techniques were observed in different studies, and this could lead to differences in analytical outcomes. Content assays focused on single marker assessments, which may be inadequate to comprehensively assess the quality of products.

CONCLUSION

This review provides knowledge of existing strengths and challenges for herbal medicine quality assessments in Africa. For future it is recommended to implement more studies on contaminants (e.g. mycotoxins) and pharmaceutical adulterants. The use of chemometrics to develop analytical methods should be promoted. Also, stakeholders in the medicine quality industry in Africa need to effectively collaborate to establish a well co-ordinated and harmonized system to provide a sustainable framework for the GACP and GMP guided production and quality assurance of herbal medicines.

Marine Natural Products in Clinical Use

Marine natural products are potent and promising sources of drugs among other natural products of plant, animal, and microbial origin. To date, 20 drugs from marine sources are in clinical use. Most approved marine compounds are antineoplastic, but some are also used for chronic neuropathic pain, for heparin overdosage, as haptens and vaccine carriers, and for omega-3 fatty-acid supplementation in the diet. Marine drugs have diverse structural characteristics and mechanisms of action. A considerable increase in the number of marine drugs approved for clinical use has occurred in the past few decades, which may be attributed to increasing research on marine compounds in laboratories across the world. In the present manuscript, we comprehensively studied all marine drugs that have been successfully used in the clinic. Researchers and clinicians are hopeful to discover many more drugs, as a large number of marine natural compounds are being investigated in preclinical and clinical studies.

Real-time fluorescence and colorimetric identification of bulbus fritillariae using recombinase assisted loop-mediated isothermal DNA amplification (RALA)

Bulbus Fritillariae (BF) is a kind of herbal medicine widely used in many countries including China, Japan, Korea, and so on. Among the known BF medicinal materials, Bulbus Fritillariae cirrhosae (BF cirrhosae) was reported to have the best curative effect. Due to the limited resources of BF cirrhosae, a lot of adulterants have emerged in the market, impairing the market order, resource development, and above all, clinical efficacy. Here, a novel nucleic acid amplification technique, Recombinase Assisted Loop-mediated isothermal DNA Amplification (RALA), was used to establish a real-time fluorescence isothermal molecular authentication method for five commonly used BF drugs. Moreover, this RALA-based assay can also be developed as a colorimetric detection method for on-site detection. Both real-time fluorescence and visual methods could detect as low as 0.1% genuine targets in the mixed samples. In summary, we report an isothermal detection system for five kinds of BF circulating in the market, providing a new choice for the molecular identification of BF drugs and showing promise in the laboratory testing as well as field identification of other herbal medicines.

Ononin: A candidate anti-parasitic drug isolated from Spatholobi caulis against infections of Dactylogyrus intermedius (Monogenea)

Dactylogyrus is a common parasitic pathogen, which causes high mortality of fish when presents in large numbers, resulting in serious economic losses. Herbal medicines contain myriad of bioactive compounds is a valuable reserve for developing safe and effective anti-parasite drugs. Here, we conducted bioassay-guided fractionation to isolate and identify the anti-parasitic constituents from Spatholobi caulis. Among five extraction solvents (petroleum ether, chloroform, ethyl acetate, methanol and water), S. caulis methanolic extract had the highest parasiticide activity in Carassius auratus, and therefore subjected to further separation and purification using multiple chromatography methods. One compound exhibiting the strongest parasiticidal activity was obtained and identified as ononin by analyzing its spectral data (NMR and ESI-MS). The EC₅₀ value of ononin against Dactylogyrus was 0.655 mg/L and showed 100% parasiticide activity with 3.0 mg/L. The 24, 48, 72, 96 h LC₅₀ for goldfish were 4.691 (the 95% CI of 4.526-4.873) mg/L, 4.612 (4.441-4.800) mg/L, 4.472 (4.345-4.607) mg/L, 4.288 (4.155-4.428) mg/L, respectively. The present results discovered for the first time that ononin had potent parasiticidal activity and have the potential to be developed as new anti-parasitic drug for the control of Dactylogyrus.

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

Integrated Strategy of Network Pharmacological Prediction and Experimental Validation Elucidate Possible Mechanism of Bu-Yang Herbs in Treating Postmenopausal Osteoporosis via ESR1

Postmenopausal osteoporosis (PMOP) is a type of bone metabolism disease-related to estrogen deficiency with an increasing incidence. Traditional Chinese (TCM) has always been used and showed effectiveness in treating PMOP. In the current study, Bu-Yang herbs were considered to be the most frequently used and efficient TCM herbs in PMOP treatment. However, chemical and pharmacological profiles were not elucidated. Network pharmacology was conducted on representative Bu-Yang herbs (Yin-Yang-Huo. Du-Zhong, Bu-Gu-Zhi, Tu-Si-Zi) to investigate the mechanism of Bu-Yang herbs on PMOP. Chemical compounds, potential targets, and disease related genes were available from the corresponding database. Results showed that Bu-Yang herbs could interact with ESR1 and estrogen signaling pathways. For further validation, the Bu-Yang decoction (BYD), formula consisted of the above-mentioned 4 Bu-Yang herbs was presented for experimental validation. In vivo, BYD significantly reversed ovariectomy (OVX)-induced osteoporosis progress in a dose-dependent manner by up-regulation of bone mineral density and amelioration of bone microarchitecture. In vitro, BYD dramatically improved the proliferation and mineral nodules formation of osteoblasts. Both in vitro and in vivo results illustrated that the phenotype change induced by BYD is correlated with up-regulated of ESR1 and activation of the β-catenin pathway. Meanwhile, inhibition of ESR1 by ICI182, 780 blocked the osteogenic phenotype and β-catenin pathway activation induced by BYD. In conclusion, the current study suggested that Bu-Yang herbs are the most useful TCM herbs in treating PMOP. Furthermore, the integrated strategy of network pharmacology prediction with experimental validation suggested that BYD exerted its anti-PMOP via ESR1 and the downstream mechanism might be activation of the β-catenin signaling pathway.

Simultaneous identification of Fritillariae cirrhosae bulbus and its common adulterants in one reaction by multiplex ligation-dependent probe amplification and high-resolution melting curve assay

Fritillariae cirrhosae bulbus, a well-known and precious medicinal and edible herb in China, causes remarkable effects on swelling and relieving cough, with fewer side effects than other congeneric medicine. It has been subject to various cheaper congeneric adulteration because of its high price and limited production. In this paper, a rapid, high throughput, sensitive and efficient technique was described for simultaneous identification of F. cirrhosae bulbus and its common adulterants by employing multiplex ligation-dependent probe amplification coupled with high-resolution melting (MLPA-HRM) curve assay in their internal transcribed spacer 1 (ITS1) regions. This assay was highly sensitive with a detection limit of 0.19 ng genomic DNA, and highly specific with no cross-reaction with common adulterants. Mixed sample analysis showed as low as 10% adulteration can be detected from F. cirrhosae bulbus in one MLPA-HRM reaction. Overall, the method described in this paper is well suited for detecting adulteration in F. cirrhosae bulbus.

Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic

Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment has become another essential means to overcome pandemics in addition to vaccine development. How to quickly find effective drugs that can control the development of a pandemic is a hot issue that still needs to be resolved in medical research today. To accelerate the development of drugs, it is necessary to target the key target proteins in the development of the pandemic, screen active molecules, and develop reliable methods for the identification and characterization of target proteins based on the active ingredients of drugs. This article discusses key target proteins and their biological mechanisms in the progression of COVID-19 and other major epidemics. We propose a model based on these foundations, which includes identifying potential core targets, screening potential active molecules of core targets, and verifying active molecules. This article summarizes the related innovative technologies and methods. We hope to provide a reference for the screening of drugs related to pandemics and the development of new drugs.

Quality standard of traditional Chinese medicines: comparison between European Pharmacopoeia and Chinese Pharmacopoeia and recent advances

Traditional Chinese medicine (TCM) are becoming more and more popular all over the world. However, quality issues of TCM may lead to medical incidents in practice and therefore quality control is essential to TCM. In this review, the state of TCM in European Pharmacopoeia are compared with that in Chinese Pharmacopoeia, and herbal drugs that are not considered as TCM and not elaborated by TCM working party at European Directorate for the Quality of Medicines & Health Care (EDQM) but present in both European Pharmacopoeia and Chinese Pharmacopoeias are also discussed. Different aspects in quality control of TCM including origins, identification, tests and assays, as well as sample preparation, marker selection and TCM processing are covered to address the importance of establishing comprehensive quality standard of TCM. Furthermore, advanced analytical techniques for quality control and standard establishment of TCM are also reviewed.

Transcriptome and complete chloroplast genome of Glycyrrhiza inflata and comparative analyses with the other two licorice species

In this study, we characterized the transcriptome and chloroplast genome of Glycyrrhiza inflata and performed comparative analyses with G. uralensis and G. glabra. 60,541unigenes were obtained from the transcriptome of G. inflata. The results of function annotation revealed a similar distribution of functional categories among three licorice species. By comparing chloroplast genomes of licorice species, it was demonstrated that the structure and the length of genome as well as gene content and gene order were highly similar. The phylogenetic tree, constructed with the mixed data of transcriptome and chloroplast genome, elucidated that G. inflata and G. glabra had a closer relationship than G. uralensis. Six regions were suggested as potential markers for the identification of three licorice species. In each licorice species, two unigenes were homologous to reference flavonol synthase. For G. inflata, 48 and 21 RNA editing sites were detected by PREP-Cp program and RNA-Seq data mapping, respectively.

Untargeted metabolomics coupled with chemometric analysis reveals species-specific steroidal alkaloids for the authentication of medicinal Fritillariae Bulbus and relevant products

Authentication of original species is embedded in the quality control system of herbal medicines. In this work, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry-based untargeted metabolomics coupled with chemometric analysis was utilized for the precise authentication of the Fritillaria species for both raw materials and commercial products. First, a stepwise difference-enlarging chemometric analysis strategy was proposed to analyze eight medicinal Fritillaria species. Subsequently, 21 species-specific markers were discovered and the specificity was investigated under different sample preparation methods. Finally, the obtained species-specific markers were successfully utilized to identify the Fritillaria species in commercially relevant products. This work is the first to report robust and specific markers for authentication of Fritillaria products, showing promise for tracking the supply chain of herbal suppliers.

Molecular Computing and Bioinformatics

Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies. Research and development in this area concerns theory, experiments, and applications of molecular computing. The core advantage of molecular computing is its potential to pack vastly more circuitry onto a microchip than silicon will ever be capable of-and to do it cheaply. Molecules are only a few nanometers in size, making it possible to manufacture chips that contain billions-even trillions-of switches and components. To develop molecular computers, computer scientists must draw on expertise in subjects not usually associated with their field, including organic chemistry, molecular biology, bioengineering, and smart materials. Bioinformatics works on the contrary; bioinformatics researchers develop novel algorithms or software tools for computing or predicting the molecular structure or function. Molecular computing and bioinformatics pay attention to the same object, and have close relationships, but work toward different orientations.