Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment

Frontiers in Pharmacology, Год журнала: 2019, Номер 10

Опубликована: Фев. 21, 2019

The research field of systems biology has greatly advanced, and as a result, the concept network pharmacology been developed. This advancement, in turn, shifted paradigm from "one-target, one-drug" mode to "network-target, multiple-component-therapeutics" mode. Network is more effective for establishing "compound-protein/gene-disease" revealing regulation principles small molecules high-throughput manner. approach makes it very powerful analysis drug combinations, especially Traditional Chinese Medicine (TCM) preparations. In this work, we first summarized databases tools currently used TCM research. Second, focused on several representative applications research, including studies compatibility, target prediction, toxicology Third, compared general statistics current evaluated search results these based 10 famous herbs. summary, rational studies, with development comprehensive have emerged but need further improvements. Additionally, given that diseases could be treated by TCMs, mediation gut microbiota, future should focus both microbiome TCMs better understand treat microbiome-related diseases.

Язык: Английский

---

ETCM: an encyclopaedia of traditional Chinese medicine

Nucleic Acids Research, Год журнала: 2018, Номер 47(D1), С. D976 - D982

Опубликована: Окт. 20, 2018

Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource drug innovation and discovery. To meet the increasing needs TCM-related data resources, we developed ETCM, Encyclopedia of Medicine. ETCM includes comprehensive standardized information commonly used herbs formulas TCM, as well their ingredients. The herb basic property quality control standard, formula composition, ingredient drug-likeness, many other provided by can serve convenient users to obtain thorough about or formula. facilitate functional mechanistic studies provides predicted target genes TCM ingredients, herbs, formulas, according chemical fingerprint similarity between ingredients known drugs. A systematic analysis function in which allows explore relationships build networks among formulas,ingredients, gene targets, related pathways diseases. freely accessible at http://www.nrc.ac.cn:9090/ETCM/. We expect develop into major warehouse promote researches development future.

Язык: Английский

---

IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics

Scientific Reports, Год журнала: 2018, Номер 8(1)

Опубликована: Март 6, 2018

Abstract Phytochemicals of medicinal plants encompass a diverse chemical space for drug discovery. India is rich with flora indigenous that have been used centuries in traditional Indian medicine to treat human maladies. A comprehensive online database on the phytochemistry will enable computational approaches towards natural product based In this direction, we present, IMPPAT, manually curated 1742 I ndian M edicinal P lants, 9596 hytochemicals, nd 1124 T herapeutic uses spanning 27074 plant-phytochemical associations and 11514 plant-therapeutic associations. Notably, curation effort led non-redundant silico library phytochemicals standard identifiers structure information. Using cheminformatic approaches, computed physicochemical, ADMET (absorption, distribution, metabolism, excretion, toxicity) drug-likeliness properties IMPPAT phytochemicals. We show stereochemical complexity shape differ from libraries commercial compounds or diversity-oriented synthesis while being similar other products. Within filtered subset 960 potential druggable phytochemicals, which majority no significant similarity existing FDA approved drugs, thus, rendering them as good candidates prospective drugs. openly accessible at: https://cb.imsc.res.in/imppat .

Язык: Английский

---

Plant-derived natural products for drug discovery: current approaches and prospects

The Nucleus, Год журнала: 2022, Номер 65(3), С. 399 - 411

Опубликована: Окт. 18, 2022

Язык: Английский

---

Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling

Drug Discovery Today, Год журнала: 2020, Номер 25(9), С. 1624 - 1638

Опубликована: Июль 12, 2020

Язык: Английский

---

The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology

Biomolecules, Год журнала: 2019, Номер 9(8), С. 362 - 362

Опубликована: Авг. 13, 2019

Natural products, including traditional herbal medicine (THM), are known to exert their therapeutic effects by acting on multiple targets, so researchers have employed network pharmacology methods decipher the potential mechanisms of THM. To conduct THM-network (THM-NP) studies, different tools and databases for constructing analyzing herb–compound–target networks. In this study, we attempted capture methodological trends in THM-NP research. We identified studies visualized combinatorial patterns. also constructed co-author affiliation networks further understand how methodologies among researchers. The results showed that number databases/tools been dramatically increased last decade, there characteristic patterns combining each analysis step studies. Overall, Traditional Chinese Medicine Systems Pharmacology Database Analysis Platform (TCMSP) was most frequently database Among processes involved research, methodology a compound–target has shown greatest change over time. summary, our describes comprehensive current ideas research design

Язык: Английский

---

IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants

ACS Omega, Год журнала: 2023, Номер 8(9), С. 8827 - 8845

Опубликована: Фев. 23, 2023

Compilation, curation, digitization, and exploration of the phytochemical space Indian medicinal plants can expedite ongoing efforts toward natural product traditional knowledge based drug discovery. To this end, we present IMPPAT 2.0, an enhanced expanded database compiling manually curated information on 4010 plants, 17,967 phytochemicals, 1095 therapeutic uses. Notably, 2.0 compiles associations at level plant parts provides a FAIR-compliant nonredundant in silico stereo-aware library phytochemicals from plants. The has been annotated with several useful properties to enable easier chemical space. We have also filtered subset 1335 drug-like which majority no similarity existing approved drugs. Using cheminformatics, characterized molecular complexity scaffold structural diversity performed comparative analysis other libraries. Altogether, is extensive atlas that accessible https://cb.imsc.res.in/imppat/.

Язык: Английский

---

HIT 2.0: an enhanced platform for Herbal Ingredients' Targets

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D1238 - D1243

Опубликована: Ноя. 15, 2021

Abstract Literature-described targets of herbal ingredients have been explored to facilitate the mechanistic study herbs, as well new drug discovery. Though several databases provided similar information, majority them are limited literatures before 2010 and need be updated urgently. HIT 2.0 was here constructed latest curated dataset focusing on Herbal Ingredients’ Targets covering PubMed 2000–2020. Currently, hosts 10 031 compound-target activity pairs with quality indicators between 2208 1237 from more than 1250 reputable herbs. The molecular cover those genes/proteins being directly/indirectly activated/inhibited, protein binders, enzymes substrates or products. Also included genes regulated under treatment individual ingredient. Crosslinks were made TTD, DrugBank, KEGG, PDB, UniProt, Pfam, NCBI, TCM-ID others. More importantly, enables automatic Target-mining My-target curation daily released literatures. Thus, users can retrieve download abstracts containing potential for interested compounds, even not yet covered in HIT. Further, log into ‘My-target’ system, curate personal target-profiling line based retrieved abstracts. accessible at http://hit2.badd-cao.net.

Язык: Английский

---

Analysis of mulberry leaf components in the treatment of diabetes using network pharmacology

European Journal of Pharmacology, Год журнала: 2018, Номер 833, С. 50 - 62

Опубликована: Май 18, 2018

Язык: Английский

---

Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches

Briefings in Bioinformatics, Год журнала: 2017, Номер 20(3), С. 806 - 824

Опубликована: Окт. 20, 2017

Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using bottom-up approach as with data-driven top-down The advent omics technologies has provided stepping-stone for emergence Bioinformatics. These provide spectrum ranging from genomics, transcriptomics proteomics to epigenomics, pharmacogenomics, metagenomics metabolomics. framework approaches are applied such data, setting level resolution well boundary system interest studying emerging properties whole rather than sum derived system's individual components. A key construction multiple networks representing each their integration layered network that exchanges within between layers. Here, we evidence how enhances computational therapeutics diagnostics, hence paving way precision medicine. aim this review familiarize reader field comprehensive overview its current state-of-the-art methods technologies. Moreover, examples success stories case studies utilize tools significantly advance research fields

Язык: Английский

---