Machine learning for synergistic network pharmacology: a comprehensive overview

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 24(3)

Published: April 6, 2023

Abstract Network pharmacology is an emerging area of systematic drug research that attempts to understand actions and interactions with multiple targets. has changed the paradigm from ‘one-target one-drug’ highly potent ‘multi-target drug’. Despite that, this synergistic approach currently facing many challenges particularly mining effective information such as targets, mechanism action, organism interaction massive, heterogeneous data. To overcome bottlenecks in multi-target discovery, computational algorithms are welcomed by scientific community. Machine learning (ML) especially its subfield deep (DL) have seen impressive advances. Techniques developed within these fields now able analyze learn huge amounts data disparate formats. In terms network pharmacology, ML can improve discovery decision making big Opportunities apply occur all stages research. Examples include screening biologically active small molecules, target identification, metabolic pathways protein–protein analysis, hub gene analysis finding binding affinity between compounds proteins. This review summarizes premier algorithmic concepts forecasts future opportunities, potential applications well several remaining implementing pharmacology. our knowledge, study provides first comprehensive assessment approaches we hope it encourages additional efforts toward development acceptance pharmaceutical industry.

Language: Английский

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Network pharmacology: a bright guiding light on the way to explore the personalized precise medication of traditional Chinese medicine

Chinese Medicine, Journal Year: 2023, Volume and Issue: 18(1)

Published: Nov. 8, 2023

Abstract Network pharmacology can ascertain the therapeutic mechanism of drugs for treating diseases at level biological targets and pathways. The effective study traditional Chinese medicine (TCM) characterized by multi-component, multi-targeted, integrative efficacy, perfectly corresponds to application network pharmacology. Currently, has been widely utilized clarify physiological activity TCM. In this review, we comprehensively summarize in TCM reveal its potential verifying phenotype underlying causes diseases, realizing personalized accurate We searched literature using “TCM pharmacology” “network as keywords from Web Science, PubMed, Google Scholar, well National Knowledge Infrastructure last decade. origins, development, are closely correlated with which applied China thousands years. have same core idea promote each other. A well-defined research strategy several aspects research, including elucidation basis syndromes, prediction targets, screening active compounds, decipherment mechanisms diseases. However, factors limit application, such selection databases algorithms, unstable quality results, lack standardization. This review aims provide references ideas encourage precise use medicine.

Language: Английский

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Advanced network pharmacology study reveals multi-pathway and multi-gene regulatory molecular mechanism of Bacopa monnieri in liver cancer based on data mining, molecular modeling, and microarray data analysis

Computers in Biology and Medicine, Journal Year: 2023, Volume and Issue: 161, P. 107059 - 107059

Published: May 21, 2023

Language: Английский

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Integrated network pharmacology and in-silico approaches to decipher the pharmacological mechanism of Selaginella tamariscina in the treatment of non-small cell lung cancer

Phytomedicine Plus, Journal Year: 2023, Volume and Issue: 3(2), P. 100419 - 100419

Published: Jan. 31, 2023

Non-small cell lung cancer (NSCLC) is a major pathological type of and accounts for more than 80% all cases. In healthcare management, it challenging to understand the mechanism NSCLC due diverse spectra limited number reported data. Selaginella tamariscina an evergreen perennial plant, hermaphrodite, used treat numerous diseases, including NSCLC. vitro research revealed therapeutic importance S. in contrast NSCLC, but molecular still unclear. present study, network pharmacology technique was employed uncover active ingredients, their potential targets, signaling pathways treatment Putative ingredients significant genes were retrieved from public database after screening. The overlapped targets among related compounds predicted using Venn plot. Following that, compound-target-disease constructed Cytoscape decipher KEGG pathway GO enrichment analysis performed investigate mechanisms treatments. Lastly, docking dynamic simulation validate interaction that exists between target proteins. findings current explored compound–target–pathway figured out Hinokiflavone, Heveaflavone, Neocryptomerin, Isocryptomerin, Apigenin, Sotetsuflavone, Cryptomerin B decisively contributed development by affecting AKT1, EGFR, VEGFA, GCK3B genes. Later, conducted successful activity against targets. concluded multi-target will help improving body's sensitivity regulating expression GCK3B, which may act as Integrated exerted promising preventive effect on acting diabetes-associated pathways. propose GSK3B are viable reduce incidence thereby exerting effects This approach introduces groundwork further protective applications drug discovery.

Language: Английский

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Challenges in phytotherapy research

Frontiers in Pharmacology, Journal Year: 2023, Volume and Issue: 14

Published: May 31, 2023

OPINION article Front. Pharmacol., 31 May 2023Sec. Ethnopharmacology Volume 14 - 2023 | https://doi.org/10.3389/fphar.2023.1199516

Language: Английский

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Metabolomics and network pharmacology reveal the mechanism of Castanopsis honey against Streptococcus pyogenes

Food Chemistry, Journal Year: 2024, Volume and Issue: 441, P. 138388 - 138388

Published: Jan. 7, 2024

Language: Английский

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IN SILICO EXPLORATION OF BERBERINE AS A POTENTIAL WOUND HEALING AGENT VIA NETWORK PHARMACOLOGY, MOLECULAR DOCKING, AND MOLECULAR DYNAMICS SIMULATION

International Journal of Applied Pharmaceutics, Journal Year: 2024, Volume and Issue: unknown, P. 188 - 194

Published: March 7, 2024

Objective: Wound healing remains a complex biological process crucial for tissue repair and homeostasis. Our goal in this paper is to focus on the application of advanced computational techniques explore potential naturally occurring compound berberine addressing molecular targets related wound healing. Methods: Network pharmacology, docking analysis, silico ADMET prediction, extensive 100 ns dynamics simulations was performed gain holistic understanding therapeutic against involved This study predicted drug-likeness scores, side effects, profiles, carcinogenicity, MolLogP, volume polar surface area berberine. Results: Findings revealed that displayed remarkable binding affinity epidermal growth factor receptor (EGFR), with energy of-8.14 kcal/mol, surpassing crystal ligand's of-7.15 kcal/mol. indicates strong modulating EGFR-related pathways critical The culmination investigation simulation, which demonstrated consistent stability over time, reinforcing as agent. Conclusion: integration gene expression enrichment studies, network docking, unveiled mechanisms underlying efficacy potent wound-healing

Language: Английский

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Coumarin: A Natural Solution for Alleviating Inflammatory Disorders

Current Research in Pharmacology and Drug Discovery, Journal Year: 2024, Volume and Issue: 7, P. 100202 - 100202

Published: Jan. 1, 2024

Coumarin, a naturally occurring compound found in various plants, has rich history of use traditional medicine. Recent research highlighted its anti-inflammatory properties, positioning it as promising candidate for treating inflammatory disorders such rheumatoid arthritis, asthma, and bowel disease. This narrative review aims to comprehensively summarize the current knowledge regarding coumarin's pharmacological effects alleviating conditions by analyzing preclinical clinical studies. The focuses on elucidating mechanisms through which coumarin exerts effects, including antioxidant activity, inhibiting pro-inflammatory cytokine production, modulation immune cell functions. Additionally, paper addresses potential limitations using coumarin, concerns about toxicity at high doses or with prolonged use. Before widespread application, further investigation is needed fully understand benefits risks.

Language: Английский

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Biomarkers for Health Functional Foods in Metabolic Dysfunction-Associated Steatotic Liver Disorder (MASLD) Prevention: An Integrative Analysis of Network Pharmacology, Gut Microbiota, and Multi-Omics

Nutrients, Journal Year: 2024, Volume and Issue: 16(18), P. 3061 - 3061

Published: Sept. 11, 2024

Metabolic dysfunction-associated steatotic liver disorder (MASLD) is increasingly prevalent globally, highlighting the need for preventive strategies and early interventions. This comprehensive review explores potential of health functional foods (HFFs) to maintain healthy function prevent MASLD through an integrative analysis network pharmacology, gut microbiota, multi-omics approaches. We first examined biomarkers associated with MASLD, emphasizing complex interplay genetic, environmental, lifestyle factors. then applied pharmacology identify food components beneficial effects on metabolic function, elucidating their action mechanisms. identifies evaluates halting or reversing development disease in stages, as well that can evaluate success failure such strategies. The crucial role microbiota its metabolites prevention homeostasis discussed. also cover state-of-the-art omics approaches, including transcriptomics, metabolomics, integrated analyses, research preventing MASLD. These advanced technologies provide deeper insights into physiological mechanisms HFF development. concludes by proposing approach developing HFFs targeting prevention, considering Korean regulatory framework. outline future directions bridge gap between basic science practical applications narrative provides a foundation researchers industry professionals interested support health. Emphasis placed maintaining balance focusing early-stage intervention

Language: Английский

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Advanced network pharmacology and molecular docking-based mechanism study to explore the multi-target pharmacological mechanism of Cymbopogon citratus against Alzheimer's disease

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 165, P. 466 - 477

Published: Jan. 11, 2024

Language: Английский

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