KampoDB, database of predicted targets and functional annotations of natural medicines

Designing combinational herbal drugs based on target space analysis

BACKGROUND

Traditional oriental medicines (TOMs) are a medical practice that follows different philosophies to pharmaceutical drugs and they have been in use for many years in different parts of the world. In this study, by integrating TOM formula and pharmaceutical drugs, we performed target space analysis between TOM formula target space and small-molecule drug target space. To do so, we manually curated 46 TOM formulas that are known to treat Anxiety, Diabetes mellitus, Epilepsy, Hypertension, Obesity, and Schizophrenia. Then, we employed Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties such as human ether-a-go-go related gene (hERG) inhibition, Carcinogenicity, and AMES toxicity to filter out potentially toxic herbal ingredients. The target space analysis was performed between TOM formula and small-molecule drugs: (i) both are known to treat the same disease, and (ii) each known to treat different diseases. Statistical significance of the overlapped target space between the TOM formula and small-molecule drugs was measured using support value. Support value distribution from randomly selected target space was calculated to validate the result. Furthermore, the Si-Wu-Tang (SWT) formula and published literature were also used to evaluate our results.

RESULT

This study tried to provide scientific evidence about the effectiveness of the TOM formula to treat the main indication with side effects that could come from the use of small-molecule drugs. The target space analysis between TOM formula and small-molecule drugs in which both are known to treat the same disease shows that many targets overlapped between the two medications with a support value of 0.84 and weighted average support of 0.72 for a TOM formula known to treat Epilepsy. Furthermore, support value distribution from randomly selected target spaces in this analysis showed that the number of overlapped targets is much higher between TOM formula and small-molecule drugs that are known to treat the same disease than in randomly selected target spaces. Moreover, scientific literature was also used to evaluate the medicinal efficacy of individual herbs.

CONCLUSION

This study provides an evidence to the effectiveness of a TOM formula to treat the main indication as well as side effects associated with the use of pharmaceutical drugs, as demonstrated through target space analysis.

Kampo herbal ointments for skin wound healing

The management of skin wound healing problems is a public health issue in which traditional herbal medicines could play a determining role. Kampo medicine, with three traditionally used ointments, provides interesting solutions for these dermatological issues. These ointments named Shiunkō, Chuōkō, and Shinsen taitsukō all have in common a lipophilic base of sesame oil and beeswax from which herbal crude drugs are extracted according to several possible manufacturing protocols. This review article brings together existing data on metabolites involved in the complex wound healing process. Among them are representatives of the botanical genera Angelica, Lithospermum, Curcuma, Phellodendron, Paeonia, Rheum, Rehmannia, Scrophularia, or Cinnamomum. Kampo provides numerous metabolites of interest, whose content in crude drugs is very sensitive to different biotic and abiotic factors and to the different extraction protocols used for these ointments. If Kampo medicine is known for its singular standardization, ointments are not well known, and research on these lipophilic formulas has not been developed due to the analytical difficulties encountered in biological and metabolomic analysis. Further research considering the complexities of these unique herbal ointments could contribute to a rationalization of Kampo's therapeutic uses for wound healing.

New approaches in developing medicinal herbs databases

Medicinal herbs databases have become a crucial part of organizing new scientific literature generated in medicinal herbs field, as well as new drug discoveries in the information era. The aim of this review was to track the current status of medicinal herbs databases. Search for finding medicinal herbs databases was carried out via Google and PubMed. PubMed was searched for papers introducing medicinal herbs databases by the recruited search strategy. Papers with an active database on the web were included in the review. Google was also searched for medicinal herbs databases. Both retrieved papers and databases were reviewed by the authors. In this review, the current status of 25 medicinal herbs databases was reviewed, and the important characteristics of databases were mentioned. The reviewed databases had a great variety in terms of characteristics and functions. Finally, some recommendations for the efficient development of medicinal herbs databases were suggested. Although contemporary medicinal herbs databases represent much useful information, adding some features to these databases could assist them to have better functionality. This work may not cover all the necessary information, but we hope that our review can provide readers with fundamental concepts, perspectives and suggestions for constructing more useful databases.

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.

Pharmacokinetic study of Ninjin'yoeito: Absorption and brain distribution of Ninjin'yoeito ingredients in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Ninjin'yoeito (NYT), a Japanese traditional Kampo medicine, has been reported to exert various clinical benefits such as relief from fatigue, malaise, anorexia, frailty, sarcopenia, and cognitive dysfunction. Recently, some review articles described the pharmacological effects of NYT and additionally indicated the possibility that multiple ingredients in NYT contribute to these effects. However, pharmacokinetic data on the ingredients are essential in addition to data on their pharmacological activities to accurately determine the active ingredients in NYT.

AIM OF THE STUDY

This study assessed the in vivo pharmacokinetics of NYT using mice.

MATERIALS AND METHODS

Target liquid chromatography-mass spectrometry (LC-MS) and wide target LC-MS or LC-tandem MS of NYT ingredients in plasma and the brain after oral administration of NYT were performed. Imaging MS was performed to investigate the detailed brain distributions of NYT ingredients.

RESULTS

The concentrations of 13 ingredients in plasma and schizandrin in the brain were quantified via target LC-MS, and the wide target analysis illustrated that several ingredients are absorbed into blood and transported into the brain. Imaging MS revealed that schizandrin was homogenously dispersed in the NYT-treated mouse brain.

CONCLUSION

These results should be useful for clarifying the active ingredients of NYT and their mechanisms of actions.

Medicine in motion: Opportunities, challenges and data analytics-based solutions for traditional medicine integration into western medical practice

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional pharmacopeias have been developed by multiple cultures and evaluated for efficacy and safety through both historical/empirical iteration and more recently through controlled studies using Western scientific paradigms and an increasing emphasis on data science methodologies for network pharmacology. Traditional medicines represent likely sources of relatively inexpensive drugs for symptomatic management as well as potential libraries of new therapeutic approaches. Leveraging this potential requires hard evidence for efficacy that separates science from pseudoscience.

MATERIALS AND METHODS

We performed a review of non-Western medical systems and developed case studies that illustrate the epistemological and practical translative barriers that hamper their transition to integration with Western approaches. We developed a new data analytics approach, in silico convergence analysis, to deconvolve modes of action, and potentially predict desirable components of TM-derived formulations based on computational consensus analysis across cultures and medical systems.

RESULTS

Abstraction, simplification and altered dose and delivery modalities were identified as factors that influence actual and perceived efficacy once a medicine is moved from a non-Western to Western setting. Case studies on these factors highlighted issues with translation between non-Western and Western epistemologies, including those where epistemological and medicinal systems drive markets that can be epicenters for zoonoses such as the novel Coronavirus. The proposed novel data science approach demonstrated the ability to identify and predict desirable medicinal components for a test indication, pain.

CONCLUSIONS

Relegation of traditional therapies to the relatively unregulated nutraceutical industry may lead healthcare providers and patients to underestimate the therapeutic potential of these medicines. We suggest three areas of emphasis for this field: First, vertical integration and embedding of traditional medicines into healthcare systems would subject them to appropriate regulation and evidence-based practice, as viable integrative implementation mode. Second, we offer a new Bradford-Hill-like framework for setting research priorities and evaluating efficacy, with the goal of rescuing potentially valuable therapies from the nutraceutical market and discrediting those that are pseudoscience. Third, data analytics pipelines offer new capacity to generate new types of TMS-inspired medicines that are rationally-designed based on integrated knowledge across cultures, and also provide an evaluative framework against which to test claims of fidelity and efficacy to TMS made for nutraceuticals.

Effects of maoto (ma-huang-tang) on host lipid mediator and transcriptome signature in influenza virus infection

Maoto, a traditional kampo medicine, has been clinically prescribed for influenza infection and is reported to relieve symptoms and tissue damage. In this study, we evaluated the effects of maoto as an herbal multi-compound medicine on host responses in a mouse model of influenza infection. On the fifth day of oral administration to mice intranasally infected with influenza virus [A/PR/8/34 (H1N1)], maoto significantly improved survival rate, decreased viral titer, and ameliorated the infection-induced phenotype as compared with control mice. Analysis of the lung and plasma transcriptome and lipid mediator metabolite profile showed that maoto altered the profile of lipid mediators derived from ω-6 and ω-3 fatty acids to restore a normal state, and significantly up-regulated the expression of macrophage- and T-cell-related genes. Collectively, these results suggest that maoto regulates the host’s inflammatory response by altering the lipid mediator profile and thereby ameliorating the symptoms of influenza.

In Vivo Pharmacokinetic Analysis Utilizing Non-Targeted and Targeted Mass Spectrometry and In Vitro Assay against Transient Receptor Potential Channels of Maobushisaishinto and Its Constituent Asiasari Radix

The Japanese traditional medicine maobushisaishinto (MBST) has been prescribed for treating upper respiratory tract infections, such as a common cold. However, its mode of action is poorly understood, especially concerning the MBST constituent Asiasari Radix (AR). In this study, we focused on AR, with an objective of clarifying its bioavailable active ingredients and role within MBST by performing pharmacokinetic and pharmacological studies. Firstly, we performed qualitative non-targeted analysis utilizing high-resolution mass spectrometry to explore the bioavailable ingredients of AR as well as quantitative targeted analysis to reveal plasma concentrations following oral administration of MBST in rats. Secondly, we performed in vitro pharmacological study of bioavailable AR ingredients in addition to other ingredients of MBST to confirm any agonistic activities against transient receptor potential (TRP) channels. As a result, methyl kakuol and other compounds derived from AR were detected in the rat plasma and showed agonistic activity against TRPA1. This study suggests that methyl kakuol as well as other compounds have the potential to be an active ingredient in AR and thus presumably would contribute in part to the effects exerted by MBST.

[Unraveling the Pathogenesis of Inflammatory Bowel Disease and Search for New Therapeutic Medicines]

The breakdown of the intestinal mucosal barrier has been shown to play a key role in the pathogenesis of intestinal immune-related disorders such as inflammatory bowel disease (IBD). IBD is a chronic inflammatory disorder with intermittent episodes of remission and relapse, and the incidence of IBD in Japan has risen dramatically in recent decades. Although sustained clinical remission has recently been recognized as an important goal of IBD therapy, there are not many treatment options to maintain long-term remission. Intestinal macrophages play pivotal roles in the regulation of immune homeostasis and inflammation in the intestine. Resident intestinal macrophages can regulate themselves and other immune cells, primarily through the spontaneous secretion of interleukin-10 (IL-10). We reported that the enhancement of IL-10 production by intestinal macrophages has the potential to be a novel therapeutic mechanism for maintaining the remission of IBD. Thus, to develop new therapeutic medicines for IBD, we screened the Wakanyaku Library derived from medicinal herbs for the ability to enhance IL-10 production by intestinal macrophages. Some compounds were identified with the potential to enhance IL-10 production by intestinal macrophages and thereby maintain long-term remission in IBD. This review focuses on our recent findings on the role of intestinal macrophages in the pathogenesis of IBD and developing a novel therapeutic strategy aimed at maintaining remission in IBD.

Closing the Gap Between Therapeutic Use and Mode of Action in Remedial Herbs

The ancient tradition of taking parts of a plant or preparing plant extracts for treating certain discomforts and maladies has long been lacking a scientific rationale to support its preparation and still widespread use in several parts of the world. In an attempt to address this challenge, we collected and integrated data connecting metabolites, plants, diseases, and proteins. A mechanistic hypothesis is generated when a metabolite is known to be present in a given plant, that plant is known to be used to treat a certain disease, that disease is known to be linked to the function of a given protein, and that protein is finally known or predicted to interact with the original metabolite. The construction of plant–protein networks from mutually connected metabolites and diseases facilitated the identification of plausible mechanisms of action for plants being used to treat analgesia, hypercholesterolemia, diarrhea, catarrh, and cough. Additional concrete examples using both experimentally known and computationally predicted, and subsequently experimentally confirmed, metabolite–protein interactions to close the connection circle between metabolites, plants, diseases, and proteins offered further proof of concept for the validity and scope of the approach to generate mode of action hypotheses for some of the therapeutic uses of remedial herbs.