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

Wang, Yixuan; Yang, Zhen; Wang, Wen-xiao; Huang, Yu‐Ning; Zhang, Qiao; Li, Jiajia; Tang, Yuping; Yue, Shi‐Jun

doi:10.1016/j.joim.2022.09.004

Cited by 12 publications

(7 citation statements)

References 117 publications

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“…In recent years, network pharmacology has been widely used in the field of traditional Chinese medicine. Researchers used network pharmacology to predict the mechanism of various diseases, providing a novel solution to TCM's ambiguous effective ingredients and mechanism (50)(51)(52). Zheng proposed an innovative highthroughput research strategy, combining computational and experimental network pharmacology methods, and selected 22 health-strengthening herbs (53).…”

Section: Discussionmentioning

confidence: 99%

Mechanism of Chaihu Longgu oyster adjusted decoction for the treatment of depression based on network pharmacology and molecular docking technology

Li¹,

Li²,

Liu³

et al. 2023

Ann Transl Med

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Background: Depression is a common clinical psychiatric disorder that is responsible for health-related disease burdens globally. According to traditional Chinese medicine (TCM), mental disorders and qi stagnation are important pathogenic mechanisms of depression. The Chaihu Longgu Oyster Decoction, which has been documented in the Shanghanlun (Treatise on Typhoid), is widely used to treat various affective disorders. Methods: Network pharmacology and molecular docking technology were used to investigate the material basis and mechanism of action of the Chaihu Longgu oyster adjusted decoction in treating depression. The main pharmacological substance bases, possible targets, and pathways of Chaihu Longgu oyster adjusted decoction in treating depression were visualized by constructing a "component-pathway-target" network. Results: Quercetin, 7-methoxy-2-methylisoflavone, baicalein, kaempferol, and lignan are the main practical chemical components in Chaihu Longgu oyster adjusted decoction. The Chaihu Longgu oyster adjusted decoction regulates 74 protein targets and 142 pathways associated with depression. Its molecular mechanism involves inhibiting neuroinflammation and improving neurotransmitter function, neuroplasticity, etc. Conclusions: The underlying mechanism of the anti-depressive effect of the Chaihu Longgu oyster adjusted decoction may involve neuroinflammatory response reduction and improvement of neurotransmitter function and neuroplasticity. This study revealed the mechanism of action of the Chaihu Longgu oyster adjusted decoction in the treatment of depression through network pharmacology, which provides a scientific basis for clinical application.

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Section: Discussionmentioning

confidence: 99%

Mechanism of Chaihu Longgu oyster adjusted decoction for the treatment of depression based on network pharmacology and molecular docking technology

Li¹,

Li²,

Liu³

et al. 2023

Ann Transl Med

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“…Botanicals are good alternatives for NSAIDs for treating fever. Currently, polyphenols and Chinese herbs are used as anti-inflammatory and antipyretic agents in patients with mild symptoms of COVID-19 [ 154 , 155 ].…”

Section: Future Perspectivesmentioning

confidence: 99%

Microbial and Host Metabolites at the Backstage of Fever: Current Knowledge about the Co-Ordinate Action of Receptors and Molecules Underlying Pathophysiology and Clinical Implications

et al. 2023

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Fever represents an elevation of body temperature, that exerts a protective effect against pathogens. Innate immune cells and neurons are implicated in the regulation of body temperature. Pathogen-associated molecular patterns, i.e., lipopolysaccharides from Gram-negative bacteria and peptidoglycan and lipoteichoic acid from Gram-positive bacteria are exogenous pyrogens, that bind to Toll-like receptors on immune and non-immune cells. The subsequent release of pro-inflammatory cytokines [interleukin-1 (IL-1), IL-6 and Tumor necrosis factor-alpha] and their passage through the brain trigger the febrile response. In fact, neurons of the pre-optic area produce prostaglandin E2 (PGE2), that, in turn, bind to the PGE2 receptors; thus, generating fever. Apart from classical non-steroidal anti-inflammatory drugs, i.e., aspirin and acetaminophen, various botanicals are currently used as antipyretic agents and, therefore, their mechanisms of action will be elucidated.

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“…Drug-Likeness (DL) ≥0. 18 were selected as candidate active ingredients [10]. The molecular structure of each active compound was confirmed by literature mining and platforms such as PubChem (https: / /pubchem.…”

Section: Candidate Compound Collection and Screeningmentioning

confidence: 99%

A computer simulation-based study on the intervention of active ingredients of Mongolian medicine into the S-protein of SARS-CoV-2-associated variant Omicron

Bao

Morigentu

et al. 2022

Preprint

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BACKGROUND: Omicron VOC (BF.7) is a variant of SARS-CoV-2 that is currently spreading globally as a dominant strain. BF.7 is more infectious than existing Omicron variants, and to date there are no specific therapeutic agents for this variant. METHODS: The active compounds were collected by TCMSP, ETCM database and literature mining method, and the targets of the compounds were searched by Swiss Target Prediction and SUPERPRED database, while the targets of Omiron virus were collected by DisGeNET and GEO database, and then the intersecting targets were compared and analyzed. In this study, Swiss-Model was applied to construct the Spike RBD structure of Omicron variant BF.7 by replacing mutant amino acids into the Native Spike (S) structure, and the structural changes of Native S were compared. The four active compounds screened were docked with Omicron S protein and Omicron S-hACE2 complexes. To evaluate the structural stability of the complexes in a physiological environment, we also performed molecular dynamics simulations of the docked complexes and compared them to the control drug, chloroquine. The affinity of ligands and protein complexes was determined by free energy analysis using the MM-PBSA algorithm, and the structural changes of S proteins in combination with ligands were evaluated. RESULTS: A total of 12 mongolic medicines were screened and 310 active ingredient predictions were made, with a total of 55 genes overlapping with Omicron variants and 14 targets with the largest differences being conserved. Once these 14 targets were mapped to the active ingredients of 12 mongolic herbs, four more precise active ingredients were filtered out. Of these four phytochemicals, Berberine was the most potent inhibitor of Omicron S protein. In addition, molecular docking simulations revealed that Berberine can bind stably to Omicron S protein and the Omicron S-hACE2 complex. Using molecular dynamics simulations, Berberine was shown to be able to form a stable complex with Omicron S in a physiological environment with better results than the control drug chloroquine. Free energy analysis by the MM-PBSA algorithm and evaluation of S protein structural changes following ligand binding also demonstrated a higher affinity of Berberine for Omicron S compared to the other small molecule compounds. CONCLUSION: Berberine was found to have the most substantial inhibitory potential against Omicron VOC (BF.7) S protein and could be further investigated and developed as a potential inhibitor of Omicron.

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

Cited by 12 publications

References 117 publications

Mechanism of Chaihu Longgu oyster adjusted decoction for the treatment of depression based on network pharmacology and molecular docking technology

Mechanism of Chaihu Longgu oyster adjusted decoction for the treatment of depression based on network pharmacology and molecular docking technology

Microbial and Host Metabolites at the Backstage of Fever: Current Knowledge about the Co-Ordinate Action of Receptors and Molecules Underlying Pathophysiology and Clinical Implications

A computer simulation-based study on the intervention of active ingredients of Mongolian medicine into the S-protein of SARS-CoV-2-associated variant Omicron

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