PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine

DCABM-TCM: A Database of Constituents Absorbed into the Blood and Metabolites of Traditional Chinese Medicine

Traditional Chinese medicine (TCM) not only maintains the health of Asian people but also provides a great resource of active natural products for modern drug development. Herein, we developed a Database of Constituents Absorbed into the Blood and Metabolites of TCM (DCABM-TCM), the first database systematically collecting blood constituents of TCM prescriptions and herbs, including prototypes and metabolites experimentally detected in the blood, together with the corresponding detailed detection conditions through manual literature mining. The DCABM-TCM has collected 1816 blood constituents with chemical structures of 192 prescriptions and 194 herbs and integrated their related annotations, including physicochemical, absorption, distribution, metabolism, excretion, and toxicity properties, and associated targets, pathways, and diseases. Furthermore, the DCABM-TCM supported two blood constituent-based analysis functions, the network pharmacology analysis for TCM molecular mechanism elucidation, and the target/pathway/disease-based screening of candidate blood constituents, herbs, or prescriptions for TCM-based drug discovery. The DCABM-TCM is freely accessible at http://bionet.ncpsb.org.cn/dcabm-tcm/. The DCABM-TCM will contribute to the elucidation of effective constituents and molecular mechanism of TCMs and the discovery of TCM-derived drug-like compounds that are both bioactive and bioavailable.

Discovery of Taxus chinensis fruit wine as potentially functional food against Alzheimer's disease by UHPLC-QE-MS/MS, network pharmacology and molecular docking

Nowadays, there is no specific cure for Alzheimer's disease (AD), but the progression of AD can be improved by preventive interventions. The wine of Taxus chinensis fruit (TCFW) has the effect of improving human immunity and anti-aging as a long history of health care wine in folk, especially popular in the longevity villages in China, which may be potentially effective dietary products to improve AD. However, the chemical constituents and molecular mechanisms of TCFW still remain unknown. In this study, chemical profiling with UHPLC-QE-MS/MS, network pharmacology and molecular docking were integrated to fastly explore the potential chemicals and mechanisms of TCFW against AD. A total of 31 chemical components in TCFW were detected and identified compared with the solvent wine of TCFW by UHPLC-QE-MS/MS. Then, 27 potential key targets and 14 chemical compounds of TCFW were uncovered for the improvement of AD by network pharmacology and molecular docking. These 14 compounds were reported to have diverse bioactivities such as neuroprotective activity, antifibrotic activity, anticancer activity, antiviral activity and effectiveness in the treatment of neuronal injury, Alzheimer's disease, etc. Among these 27 targets affected by TCFW predicted by our approach, AKT1, PTGS2, NOS3, NOS2, INS, ESR1, ESR2, BDNF, IL6, IL1B, DRD2 and ACHE were significantly altered in AD. The GO and KEGG enrichment analyses revealed that TCFW mainly acted on oxidative response, inflammatory response, insulin secretion, amyloid fibril formation, neurodegenerative pathway-multiple diseases, Alzheimer's disease, longevity regulation pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, etc, which were the main pathogenesis of AD. PRACTICAL APPLICATIONS: Alzheimer's disease (AD) is a degenerative neurological disorder characterized by cognitive and behavioral dysfunction. Nowadays, there is no specific cure for AD, but the progression of AD can be improved by preventive interventions. The wine of Taxus chinensis fruit (TCFW) has the effect of improving human immunity and anti-aging as a long history of health care wine in folk, especially popular in the longevity villages in China, which may be potentially effective dietary products to improve AD. This study proposed a fastly integrated method to explore the potential chemicals and mechanisms of TCFW against AD by UHPLC-QE-MS/MS, network pharmacology and molecular docking. Here, we found that TCFW may ameliorate AD by reversing many biological events, including oxidative stress, inflammatory response, neuronal apoptosis, insulin secretion, amyloid fibril formation, and T cell co-stimulation, which may provide some insights for the development and research of anti-AD drugs.

Methodology of network pharmacology for research on Chinese herbal medicine against COVID-19: A review

Traditional Chinese medicine, as a complementary and alternative medicine, has been practiced for thousands of years in China and possesses remarkable clinical efficacy. Thus, systematic analysis and examination of the mechanistic links between Chinese herbal medicine (CHM) and the complex human body can benefit contemporary understandings by carrying out qualitative and quantitative analysis. With increasing attention, the approach of network pharmacology has begun to unveil the mystery of CHM by constructing the heterogeneous network relationship of "herb-compound-target-pathway," which corresponds to the holistic mechanisms of CHM. By integrating computational techniques into network pharmacology, the efficiency and accuracy of active compound screening and target fishing have been improved at an unprecedented pace. This review dissects the core innovations to the network pharmacology approach that were developed in the years since 2015 and highlights how this tool has been applied to understanding the coronavirus disease 2019 and refining the clinical use of CHM to combat it.

Dementia key gene identification with multi-layered SNP-gene-disease network

MOTIVATION

Recently, various approaches for diagnosing and treating dementia have received significant attention, especially in identifying key genes that are crucial for dementia. If the mutations of such key genes could be tracked, it would be possible to predict the time of onset of dementia and significantly aid in developing drugs to treat dementia. However, gene finding involves tremendous cost, time and effort. To alleviate these problems, research on utilizing computational biology to decrease the search space of candidate genes is actively conducted.

In this study, we propose a framework in which diseases, genes and single-nucleotide polymorphisms are represented by a layered network, and key genes are predicted by a machine learning algorithm. The algorithm utilizes a network-based semi-supervised learning model that can be applied to layered data structures.

RESULTS

The proposed method was applied to a dataset extracted from public databases related to diseases and genes with data collected from 186 patients. A portion of key genes obtained using the proposed method was verified in silico through PubMed literature, and the remaining genes were left as possible candidate genes.

AVAILABILITY AND IMPLEMENTATION

The code for the framework will be available at http://www.alphaminers.net/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Literature based discovery of alternative TCM medicine for adverse reactions to depression drugs

Background

In recent years, Traditional Chinese Medicine (TCM) and alternative medicine have been widely used along with western drugs as a complementary form of treatment. In this study, we first use the scientific literature to identify western drugs with obvious side effects. Then, we find TCM alternatives for these western drugs to ameliorate their side effects.

Results

We used depression as a case study. To evaluate our method, we showed the relation between herb-ingredients-target-disease for representative alternative herbs of western drugs. Further, a protein-protein interaction network of western drugs and alternative herbs was produced, and we performed enrichment analysis of the targets of the active ingredients of the herbs and examined the enrichment of Gene Ontology terms for Biological Process, Cellular Component, and Molecular Function and KEGG Pathway levels, to show how these targets affect different levels of gene expression.

Conclusion

Our proposed method is able to select herbs that are highly relevant to the target indication (depression) and are able to treat the side effects caused by the target drug. The compounds from our selected alternative herbal medicines can therefore be complementary to the western drugs and ameliorate their side effects, which may help in the development of new drugs.

eHealth technologies assisting in identifying potential adverse interactions with complementary and alternative medicine (CAM) or standalone CAM adverse events or side effects: a scoping review

BACKGROUND

While there are several existing eHealth technologies for drug-drug interactions and stand-alone drug adverse effects, it appears that considerably less attention is focussed on that of complementary and alternative medicine (CAM). Despite poor knowledge of their potential interactions and side effects, many patients use CAM. This justifies the need to identify what eHealth technologies are assisting in identifying potential 1) adverse drug interactions with CAM, 2) adverse CAM-CAM interactions or 3) standalone CAM adverse events or side effects.

METHODS

A scoping review was conducted to identify eHealth technologies assisting in identifying potential adverse interactions with CAM or standalone CAM adverse events or side effects, following Arksey and O'Malley's five-stage scoping review framework. MEDLINE, EMBASE, and AMED databases and the Canadian Agency for Drugs and Technologies in Health website were systematically searched. Eligible articles had to have assessed or referenced an eHealth technology assisting in identifying potential one or more of the three aforementioned items. We placed no eligibility restrictions on type of eHealth technology.

RESULTS

Searches identified 3467 items, of which 2763 were unique, and 2674 titles and abstracts were eliminated, leaving 89 full-text articles to be considered. Of those, 48 were not eligible, leaving a total of 41 articles eligible for review. From these 41 articles, 69 unique eHealth technologies meeting our eligibility criteria were identified. Themes which emerged from our analysis included the following: the lack of recent reviews of CAM-related healthcare information; a large number of databases; and the presence of government adverse drug/event surveillance.

CONCLUSIONS

The present scoping review is the first, to our knowledge, to provide a descriptive map of the literature and eHealth technologies relating to our research question. We highlight that while an ample number of resources are available to healthcare providers, researchers, and patients, we caution that the quality and update frequency for many of these resources vary widely, and until formally assessed, remain unknown. We identify that a need exists to conduct an updated and systematically-searched review of CAM-related healthcare or research resources, as well as develop guidance documents associated with the development and evaluation of CAM-related eHealth technologies.

Cangfu daotan decoction for polycystic ovary syndrome: A protocol of systematic review and meta-analysis

BACKGROUNDS

Polycystic ovary syndrome (PCOS) is common endocrine disorder in women and can lead to serious social burdens associated with various reproductive and metabolic abnormalities. Existing therapy is controversial in its effectiveness including side effects. In traditional Korean Medicine, Cangfu Daotan Decoction (CDD), also known as Changbudodam-tang, is used for PCOS patients who are in the type of stagnation of phlegm and dampness. In this study, we aimed to evaluate the efficacy and safety of CDD for PCOS as alternative treatment.

METHODS

Two researchers will search the following databases from their inception to February 2019 for relevant randomized controlled trials (RCTs): The Cochrane Library, PubMed, EMBASE, Chinese National Knowledge Infrastructure Database (CNKI), and 5 Korean medical databases (Korean Studies Information Service System, KoreaMed, DBPIA, Oriental Medicine Advanced Searching Integrated System, and Research Information Service System). The primary outcome will be the scales that assessed drug efficacy including total response rate, sex hormone level (LH, FSH, Testosterone, LH/FSH ratio), BMI, ovulation rate, and pregnancy rate. Adverse events will be assessed as the secondary outcome. Study selection, data extraction, and assessment of risk of bias will be conducted by 2 researchers independently. Statistical analysis will be performed by using the Cochrane Review Manager (RevMan 5.3) software.

RESULTS AND CONCLUSION

This review will provide the latest knowledge and evidence on the efficacy and safety of CDD for PCOS women through the analysis of various evaluation scales.

ETHICS AND DISSEMINATION

This systematic review does not require ethical approval and will be published in a peer-reviewed journal.

PROSPERO REGISTRATION NUMBER

CRD42019134270.

Utilisation of Electronic Health Records for Public Health in Asia: A Review of Success Factors and Potential Challenges

INTRODUCTION

Electronic health records offer a valuable resource to improve health surveillance and evaluation as well as informing clinical decision making. They have been introduced in many different settings, including low- and middle-income countries, yet little is known of the progress and effectiveness of similar information systems within Asia. This study examines the implementation of EHR systems for use at a population health level in Asia and to identify their current role within public health, key success factors, and potential barriers in implementation.

MATERIAL AND METHODS

A systematic search process was implemented. Five databases were searched with MeSH key terms and Boolean phrases. Articles selected for this review were based on hospital provider electronic records with a component of implementation, utilisation, or evaluation for health systems or at least beyond direct patient care. A proposed analytic framework considered three interactive components: the content, the process, and the context.

RESULTS

Thirty-two articles were included in the review. Evidence suggests that benefits are significant but identifying and addressing potential challenges are critical for success. A comprehensive preparation process is necessary to implement an effective and flexible system.

DISCUSSION

Electronic health records implemented for public health can allow the identification of disease patterns, seasonality, and global trends as well as risks to vulnerable populations. Addressing implementation challenges will facilitate the development and efficacy of public health initiatives in Asia to identify current health needs and mitigate future risks.

Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine

Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies. We applied a systems pharmacology approach to prioritize disease-target genes. Using this bioinformatics approach, we analyzed 14,713 GWAS disease-TCM-target gene pairs and identified 115 disease-gene pairs with q value < 0.2. We validated several of these GWAS disease-TCM-target gene pairs with literature evidence, demonstrating that this computational approach could reveal novel indications for TCM. We also develop TCM-Disease web application to facilitate the traditional Chinese medicine drug repurposing efforts. Systems pharmacology is a promising approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. The computational approaches described in this study could be easily expandable to other disease-gene network analysis.