TM-MC 2.0: an enhanced chemical database of medicinal materials in Northeast Asian traditional medicine.

BACKGROUND: As chromatographic techniques have advanced, many articles that analyze the constituting compounds of medicinal materials have been published in relation to Northeast Asian traditional medicine, including traditional Chinese medicine (TCM). TM-MC was launched in 2015, providing information about the chemical compounds in medicinal materials from chromatographic articles in PubMed. Since 2015, through continuous curation efforts, we have now released TM-MC 2.0 with significant improvements to the quantity and quality of the data ( https://tm-mc.kr ). DESCRIPTION: TM-MC 2.0 contains 635 medicinal materials, 34,107 chemical compounds (21,306 identified and de-duplicated), 13,992 targets, 27,997 diseases, and 5,075 prescriptions (2,393 de-duplicated by name). The database provides the largest number of identified compounds for medicinal materials listed in the pharmacopoeia compared to all TCM databases. In particular, marker compounds of medicinal materials and many newly discovered compounds were added through the manual curation of recent chromatographic articles. CONCLUSION: TM-MC 2.0 provides the largest collection of information about the chemical compounds of the medicinal materials listed in the Korean, Chinese, and Japanese pharmacopoeias. Our database can be utilized for network pharmacology in traditional medicine and for the compound screening of medicinal materials for modern drug discovery.

Epigenetic mechanisms involved in the neuroprotective effect of scorpion extract in a Parkinson's disease murine model based on multi-omics approach.

OBJECTIVE: To investigate whether scorpion extract elicits a neuroprotective effect in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice models, and the genes associated with the therapeutic effects using RNA sequencing (seq) analysis. METHODS: This study investigated the changes in interaction between messenger ribonucleic acid (mRNA) expression and deoxyribonucleic acid (DNA) methylation related to the protective effects of scorpion extracts, in the substantia nigra (SN) region of a MPTP-induced Parkinson's disease (PD) model. RESULTS: In this model, scorpion extracts attenuated the motor impairment as demonstrated by the rotarod and open field tests. Scorpion extracts consistently attenuated the decrease of tyrosine hydroxylase (TH) positive neural cells in the SN and striatum of mice. We profiled genome- wide DNA methylation using Methyl-Seq and measured the transcriptome using RNA-Seq in murine SN in the following groups: vehicle-treated MPTP-induced PD mice and scorpion extract- treated MPTP-induced PD mice. In total, 13 479 differentially expressed genes were identified in association with the anti-PD effect of the scorpion extract, mainly in the promoter and coding regions. Among them, 47 were negatively correlated down- regulated genes. Nineteen genes out of 47 down- regulated genes were negatively correlated with the expression of the other 28 genes. Among these genes, SGSM1 was related to dopaminergic neu- rons including dopamine transporters, TH, dihy- droxyphenylalanine decarboxylase, and dopamine D2 receptor. CONCLUSION: This study provides insights into the anti-parkinsonian effects of scorpion extract and reveals the epigenetic targets in its therapeutic mechanism.

Identification of Epigenetic Mechanisms Involved in the Anti-Asthmatic Effects of Descurainia sophia Seed Extract Based on a Multi-Omics Approach.

Asthma, a heterogeneous disease of the airways, is common around the world, but little is known about the molecular mechanisms underlying the interactions between DNA methylation and gene expression in relation to this disease. The seeds of Descurainia sophia are traditionally used to treat coughs, asthma and edema, but their effects on asthma have not been investigated by multi-omics analysis. We undertook this study to assess the epigenetic effects of ethanol extract of D. sophia seeds (DSE) in an ovalbumin (OVA)-induced mouse model of asthma. We profiled genome-wide DNA methylation by Methyl-seq and characterized the transcriptome by RNA-seq in mouse lung tissue under three conditions: saline control, OVA-induced, and DSE-treated. In total, 1995 differentially methylated regions (DMRs) were identified in association with anti-asthmatic effects, most in promoter and coding regions. Among them, 25 DMRs were negatively correlated with the expression of the corresponding 18 genes. These genes were related to development of the lung, respiratory tube and respiratory system. Our findings provide insights into the anti-asthmatic effects of D. sophia seeds and reveal the epigenetic targets of anti-inflammatory processes in mice.

A data mining approach to selecting herbs with similar efficacy: Targeted selection methods based on medical subject headings (MeSH).

ETHNO-PHARMACOLOGICAL RELEVANCE: Natural products have long been the most important source of ingredients in the discovery of new drugs. Moreover, since the Nagoya Protocol, finding alternative herbs with similar efficacy in traditional medicine has become a very important issue. Although random selection is a common method of finding ethno-medicinal herbs of similar efficacy, it proved to be less effective; therefore, this paper proposes a novel targeted selection method using data mining approaches in the MEDLINE database in order to identify and select herbs with a similar degree of efficacy. MATERIALS AND METHODS: From among sixteen categories of medical subject headings (MeSH) descriptors, three categories containing terms related to herbal compounds, efficacy, toxicity, and the metabolic process were selected. In order to select herbs of similar efficacy in a targeted way, we adopted the similarity measurement method based on MeSH. In order to evaluate the proposed algorithm, we built up three different validation datasets which contain lists of original herbs and corresponding medicinal herbs of similar efficacy. RESULTS: The average area under curve (AUC) of the proposed algorithm was found to be about 500% larger than the random selection method. We found that the proposed algorithm puts more hits at the front of the top-10 list than the random selection method, and precisely discerns the efficacy of the herbs. It was also found that the AUC of the experiments either remained the same or increased slightly in all three validation datasets as the search range was increased. CONCLUSION: This study reveals and proves that the proposed algorithm is significantly more accurate and efficient in finding alternative herbs of similar efficacy than the random selection method. As such, it is hoped that this approach will be used in diverse applications in the ethno-pharmacology field.

Comparative analysis of web search trends between experts and public for medicinal herbs in Korea.

ETHNOPHARMACOLOGICAL RELEVANCE: The information and knowledge about ethno-medicinal herbs are getting stronger interest in Global and Korea after the agreement of the Nagoya Protocol. However, it is known that there is a serious asymmetry of ethno-medicinal information between experts and public, thus this study aimed to analyze the similarities and differences in interest between experts and public for medicinal herbs in Korea through big data analysis. MATERIALS AND METHODS: The medicinal herbs selected in this study were the top 10 herbs in terms of the amounts purchased by TKM centers. And two representative web search engines were selected to collect the web search logs, i.e. big data, of experts and public for medicinal herbs in Korea. Comparative analysis was accomplished through descriptive statistical analysis, Pearson's correlation coefficient, and time-series graph analysis. RESULTS: The web search traffic logs were collected for the past three years (2012-2014) from OASIS and NAVER, which are the representative web search engines of experts and public respectively in Korea. First, regarding OASIS, the most searched medicinal herb was Angelicae Gigantis Radix while the least searched was Alismatis Rhizoma; for NAVER, the most searched medicinal herb was Paeoniae Radix, unlike OASIS, and the least searched was Alismatis Rhizoma, as with OASIS. The coefficient between rank of herbs and OASIS was -0.401, and that between rank of herbs and NAVER was -0.387, and the correlational coefficient for web search trends of OASIS and NAVER during the past three years was 0.438. Also the correlation of interest between experts and public for each herb on monthly web trends basis was similar with regard to Glycyrrhizae Radix et Rhizoma and Angelicae Gigantis Radix, but different with regard to the other 8 medicinal herbs. Finally, significant outcomes or suggestions were figured out through time-series graph analysis. CONCLUSION: This study presents meaningful results concerning the similarities and differences in interest between experts and public for popular medicinal herbs in Korea. Contrary to the common assumption that there exists big different interest between experts and public, this study revealed that there is apparent similar interest between experts and public on popular medicinal herbs in Korea.