Systems pharmacology and molecular docking strategies prioritize natural molecules as antiinflammatory agents

2021 ◽  
pp. 283-319
Author(s):  
Anjana S. Nair ◽  
Anupam Paliwal
Keyword(s):  
Molecular Docking ◽  
Systems Pharmacology ◽  
Antiinflammatory Agents

scholarly journals Elucidating the Mechanisms of Action of Lianhua Qingwen decoction for the Treatment of COVID-19 via Systems Pharmacology Approaches

2021 ◽  
Author(s):  
Xiting Wang ◽  
Tao Lu
Keyword(s):  
Molecular Docking ◽  
Blood Circulation ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Detection Algorithm ◽  
Network Pharmacology ◽  
Systems Pharmacology ◽  
Protein Protein Interaction ◽  
Further Development ◽  
Protein Protein Interaction Network

Abstract Due to the severity of the COVID-19 epidemic, to identify a proper treatment for COVID-19 is of great significance. Traditional Chinese Medicine (TCM) has shown its great potential in the prevention and treatment of COVID-19. One of TCM decoction, Lianhua Qingwen decoction displayed promising treating efficacy. Nevertheless, the underlying molecular mechanism has not been explored for further development and treatment. Through systems pharmacology and network pharmacology approaches, we explored the potential mechanisms of Lianhua Qingwen treating COVID-19 and acting ingredients of Lianhua Qingwen decoction for COVID-19 treatment. Through this way, we generated an ingredients-targets database. We also used molecular docking to screen possible active ingredients. Also, we applied the protein-protein interaction network and detection algorithm to identify relevant protein groupings of Lianhua Qingwen. Totally, 605 ingredients and 1,089 targets were obtained. Molecular Docking analyses revealed that 35 components may be the promising acting ingredients, 7 of which were underlined according to the comprehensive analysis. Our enrichment analysis of the 7 highlighted ingredients showed relevant significant pathways that could be highly related to their potential mechanisms, e.g. oxidative stress response, inflammation, and blood circulation. In summary, this study suggests the promising mechanism of the Lianhua Qingwen decoction for COVID-19 treatment. Further experimental and clinical verifications are still needed.

scholarly journals Prediction of the Antiinflammatory Activity of New S-alkyl Derivatives of 1,2,4-triazol-3-thiones Using the PASS Computer Program and Molecular Docking

2020 ◽  
Vol 3 (1) ◽  
pp. 36-43
Author(s):  
Natalya Mykolaivna Chalenko ◽  
Anna Olegovna Syrovaya ◽  
Natalya P Kobzar ◽  
Maryna V Rakhimova ◽  
Irina A Sych ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiinflammatory Activity ◽  
Basic Structure ◽  
Virtual Library ◽  
Antiinflammatory Agents ◽  
Group 4 ◽  
Alkyl Derivatives ◽  
Cox 2 ◽  
Cox 2 Inhibitors ◽  
Derivatives Of

The strategy of rational approaches to the search for selective COX-2 inhibitors as potential antiinflammatory agents has been proposed and elaborated. It is based on the use of PASS-prediction and molecular docking. The choice of the basic structure of 4-amino-3-thio-1,2,4-triazole as a promising object of chemical modification has been substantiated. Using a modification of the primary molecule, a virtual library of S-derivatives of 5-substituted 4-amino(pyrrol)3-thio-4H-1,2,4-triazoles in the amount of 100 compounds (ten groups) has been obtained by introducing various pharmacophore fragments. Based on the analysis of the results of the PASS-prediction and molecular docking, six of the ten planned groups of compounds have been selected for the synthesis as promising selective COX-2 inhibitors. The reliability of the prediction results has already been confirmed for one of the promising group 4-amino-5-(pyridine-4-yl)-1,2,4-triazole (4?)-3-yl-thioacetamides.

scholarly journals Integrative Analysis of Systems Pharmacology and Proteomics to Identify Key Targets and Pathways of Tuomin-Zhiti-Decoction for Allergic Rhinitis

2021 ◽  
Author(s):  
Jinjun Cheng ◽  
Meiling Zhang ◽  
Yanfei Zheng ◽  
Ji Wang ◽  
Qi Wang
Keyword(s):  
Allergic Rhinitis ◽  
Molecular Docking ◽  
Immunoglobulin E ◽  
Therapeutic Potential ◽  
Function Analysis ◽  
Underlying Mechanism ◽  
Systems Pharmacology ◽  
Proteomics Analysis ◽  
Active Compounds ◽  
Nasal Symptoms

Abstract Background: Tuomin-Zhiti-Decoction (TZD) is a polyherbal medicine consisting of eleven different herbs and has a significant effect on Allergic rhinitis (AR), yet its underlying mechanism is still unknown. Methods: Mice were sensitized and intranasally challenged with ovalbumin (OVA), the nasal symptoms, Th1/Th2-related cytokines and histopathology were examinated after TZD treatments. Bio-active compounds, potential therapeutic targets and underlying mechanisms of TZD against AR were systematically elucidated by integrating systems pharmacology approach and proteomics analysis. Then we validated the binding affinity between key targets and their corresponding active compounds using molecular docking evaluation.Results: A total of 280 active ingredients, 240 targets of TZD and 643 AR-related targets were obtained. Furthermore, 74 overlapping targets were identified. TZD oral administrations inhibited allergic responses via reduction of OVA-specific immunoglobulin E (IgE) levels and histamine release. In nasal tissue, TZD not only decreased nasal rubbing and sneezing to AR mice, but also reduced AR-induced damage to nasal mucosa, accordingly, the nasal symptoms were also clearly ameliorated. Moreover, TZD modulated the balance of Th1/Th2/Th17. The proteomics analysis identified 41 differentially expressed proteins (DEPs), protein function analysis showed that the DEPs were mainly involved in PI3K-AKT, MAPK, EGFR tyrosine kinase inhibitor resistance, NF-kappa B signaling pathway. Our results indicate that TZD plays important roles by restoring DEPs, through the selection of key DEPs, IL-6 and CD40 may be potential protein targets of TZD in treatment of AR. Combining the systems pharmacology, quercetin and wogonin may play more effective roles in AR. Molecular docking confirmed that most active compounds of TZD could bind tightly to the key targets.Conclusion: TZD may have therapeutic potential for treating AR, integrating analysis of systems pharmacology and proteomics uncovered the underlying mechanism and targets of TZD, which provides a scientific method for the rational development of traditional Chinese medicine.

Systems pharmacology and molecular docking strategies prioritize natural molecules as cardioprotective agents

RSC Advances ◽  
2015 ◽  
Vol 5 (94) ◽  
pp. 77042-77055 ◽  
Author(s):  
Jeganathan Manivannan ◽  
Thangarasu Silambarasan ◽  
Rajendran Kadarkarairaj ◽  
Boobalan Raja
Keyword(s):  
Molecular Docking ◽  
Natural Compounds ◽  
Systems Pharmacology

Multidimensional prioritization of cardioprotective natural compounds.

scholarly journals The System Research of the Molecular Mechanism of Quyushengxin Capsule in the Treatment of Osteonecrosis of the Femoral Head

2022 ◽  
Vol 2022 ◽  
pp. 1-11
Author(s):  
Xia Du ◽  
Lintao Zhao ◽  
Yuan Qiao ◽  
Yuan Liu ◽  
Dong Guo
Keyword(s):  
Molecular Docking ◽  
Femoral Head ◽  
Molecular Mechanism ◽  
Enrichment Analysis ◽  
Integrated Approach ◽  
Pathway Enrichment Analysis ◽  
Systems Pharmacology ◽  
Protein Protein Interaction ◽  
Chip Experiment ◽  
Tnf Α

Osteonecrosis of the femoral head (ONFH) is a chronic and irreversible disease that has a risk of eventually developing into a joint collapse and resulting in joint dysfunction. Quyushengxin capsule (QYSXC) is an effective and safe traditional Chinese medicine used in the treatment of ONFH. In this present study, an integrated approach was used to investigate the mechanism of QYSXC in the treatment of ONFH, which contained systems pharmacology, molecular docking, and chip experiment. In the systems pharmacology, target fishing, protein-protein interaction (PPI), Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis, and herbs-compounds-targets-pathways (H-C-T-P) network construction were performed to study the mechanism of QYSXC in the treatment of ONFH. The results showed that 15 key compounds, 8 key targets, and 8 key signaling pathways were found for QYSXC in the treatment with ONFH. Then, molecular docking was performed to further explore the interaction between some key compounds and key targets. After that, the chip experiment was performed to verify some target factors, including ICAM-1, IL-6, IL-1α, IL-1β, IL-2, IL-4, IL-10, and TNF-α. The results of this work may provide a theoretical basis for further research on the molecular mechanism of QYSXC in the treatment of ONFH.

Dissection of effect mechanisms of Kudiezi injection against myocardial ischemia based on virtual screening and systems pharmacology approach

2020 ◽  
Author(s):  
Rongfang Xie ◽  
Zhenzhen Liu ◽  
Peiying Shi ◽  
Zuan Lin ◽  
Bing Chen ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Myocardial Ischemia ◽  
Molecular Mechanisms ◽  
Fluid Shear Stress ◽  
Scientific Basis ◽  
Therapeutic Effects ◽  
Systems Pharmacology ◽  
Preparation Methods ◽  
Kegg Pathways

Abstract Background Kudiezi (KDZ) injection, a Chinese medicine preparation, has been widely used for the treatment of myocardial injury in recent years. However, the knowledge of the molecular mechanisms is limited to support its clinical application. It is of great importance to explore the underlying mechanisms of this preparation. Methods In this research, the 10 main ingredients in this injection were identified firstly by HPLC-Q-TOF-MS. Afterwards, virtual screening and an integrated systems pharmacology approach combined with molecular docking (molecular docking software: Sybyl-X 1.3 and Autodock vina) were adopted to predict its therapeutic mechanisms. Results 7 proteins targets and 9 KEGG pathways, possessing highly relevance to the therapeutic effects of KDZ against MI, were predicted reasonably. The systems analysis suggested that KDZ injection could exert its therapeutic effects against myocardial ischemia possibly through multi-targets including EGFR, MAPK10, SRC, et al, and multi-pathways referring to MAPK, Focal adhesion, Complement and coagulation cascades, Fluid shear stress and atherosclerosis, etc. Conclusion This research provided a scientific basis to clarify the comprehensive pharmacological mechanism of KDZ injection acting on MI, and could provide valuable clues on considering the active ingredient KDZ-6 as a multi-targets leading compound.

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