Network pharmacology based virtual screening of Flavonoids from Dodonea angustifolia and the molecular mechanism against inflammation

Alamri, Mubarak A.; Tahir ul Qamar, Muhammad

doi:10.1016/j.jsps.2023.101802

Cited by 6 publications

(2 citation statements)

References 46 publications

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“…The fundamental components of a biological system are genes and the products they produce, which interact randomly to form a complex network ( Alamri and ul Qamar, 2023 ). Understanding immunology, the mechanisms of defense, signaling tasks, modes of transportation, and the onset of diseases more thoroughly can be accomplished by analyzing both genes and protein expression.…”

Section: Resultsmentioning

confidence: 99%

System biology approach to identify the novel biomarkers in glioblastoma multiforme tumors by using computational analysis

Alqahtani,

Altharawi,

Alabbas

et al. 2024

Front. Pharmacol.

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Introduction: The most common primary brain tumor in adults is glioblastoma multiforme (GBM), accounting for 45.2% of all cases. The characteristics of GBM, a highly aggressive brain tumor, include rapid cell division and a propensity for necrosis. Regretfully, the prognosis is extremely poor, with only 5.5% of patients surviving after diagnosis.Methodology: To eradicate these kinds of complicated diseases, significant focus is placed on developing more effective drugs and pinpointing precise pharmacological targets. Finding appropriate biomarkers for drug discovery entails considering a variety of factors, including illness states, gene expression levels, and interactions between proteins. Using statistical techniques like p-values and false discovery rates, we identified differentially expressed genes (DEGs) as the first step in our research for identifying promising biomarkers in GBM. Of the 132 genes, 13 showed upregulation, and only 29 showed unique downregulation. No statistically significant changes in the expression of the remaining genes were observed.Results: Matrix metallopeptidase 9 (MMP9) had the greatest degree in the hub biomarker gene identification, followed by (periostin (POSTN) at 11 and Hes family BHLH transcription factor 5 (HES5) at 9. The significance of the identification of each hub biomarker gene in the initiation and advancement of glioblastoma multiforme was brought to light by the survival analysis. Many of these genes participate in signaling networks and function in extracellular areas, as demonstrated by the enrichment analysis.We also identified the transcription factors and kinases that control proteins in the proteinprotein interactions (PPIs) of the DEGs.Discussion: We discovered drugs connected to every hub biomarker. It is an appealing therapeutic target for inhibiting MMP9 involved in GBM. Molecular docking investigations indicated that the chosen complexes (carmustine, lomustine, marimastat, and temozolomide) had high binding affinities of −6.3, −7.4, −7.7, and −8.7 kcal/mol, respectively, the mean root-mean-square deviation (RMSD) value for the carmustine complex and marimastat complex was 4.2 Å and 4.9 Å, respectively, and the lomustine and temozolomide complex system showed an average RMSD of 1.2 Å and 1.6 Å, respectively. Additionally, high stability in root-mean-square fluctuation (RMSF) analysis was observed with no structural conformational changes among the atomic molecules. Thus, these in silico investigations develop a new way for experimentalists to target lethal diseases in future.

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Section: Resultsmentioning

confidence: 99%

System biology approach to identify the novel biomarkers in glioblastoma multiforme tumors by using computational analysis

Alqahtani,

Altharawi,

Alabbas

et al. 2024

Front. Pharmacol.

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show abstract

“…Alamri et al [26] used network pharmacology and molecular docking technology to demonstrate that the active ingredient 5-Hydroxy-7,8 dimethoxyflavone in D. angustifolia can bind to AKT1, VEGFA, and EGFR, thereby participating in the body's inflammatory response. Minjee et al [27] used network pharmacology and molecular docking to identify the potential compounds and targets of Fritillariae thunbergii for treating influenza-related inflammation.…”

Section: Introductionmentioning

confidence: 99%

Study of the Anti-Inflammatory Mechanism of β-Carotene Based on Network Pharmacology

Wu,

Chen,

Chen

et al. 2023

Molecules

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β-carotene is known to have pharmacological effects such as anti-inflammatory, antioxidant, and anti-tumor properties. However, its main mechanism and related signaling pathways in the treatment of inflammation are still unclear. In this study, component target prediction was performed by using literature retrieval and the SwissTargetPrediction database. Disease targets were collected from various databases, including DisGeNET, OMIM, Drug Bank, and GeneCards. A protein–protein interaction (PPI) network was constructed, and enrichment analysis of gene ontology and biological pathways was carried out for important targets. The analysis showed that there were 191 unique targets of β-carotene after removing repeat sites. A total of 2067 targets from the three databases were integrated, 58 duplicate targets were removed, and 2009 potential disease action targets were obtained. Biological function enrichment analysis revealed 284 biological process (BP) entries, 31 cellular component (CC) entries, 55 molecular function (MF) entries, and 84 cellular pathways. The biological processes were mostly associated with various pathways and their regulation, whereas the cell components were mainly membrane components. The main molecular functions included RNA polymerase II transcription factor activity, DNA binding specific to the ligand activation sequence, DNA binding, steroid binding sequence-specific DNA binding, enzyme binding, and steroid hormone receptors. The pathways involved in the process included the TNF signaling pathway, sphingomyelin signaling pathway, and some disease pathways. Lastly, the anti-inflammatory signaling pathway of β-carotene was systematically analyzed using network pharmacology, while the molecular mechanism of β-carotene was further explored by molecular docking. In this study, the anti-inflammatory mechanism of β-carotene was preliminarily explored and predicted by bioinformatics methods, and further experiments will be designed to verify and confirm the predicted results, in order to finally reveal the anti-inflammatory mechanism of β-carotene.

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Potential of natural products in inflammation: biological activities, structure–activity relationships, and mechanistic targets

Guo,

Peng,

Liu

et al. 2024

Arch. Pharm. Res.

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Network pharmacology based virtual screening of Flavonoids from Dodonea angustifolia and the molecular mechanism against inflammation

Cited by 6 publications

References 46 publications

System biology approach to identify the novel biomarkers in glioblastoma multiforme tumors by using computational analysis

System biology approach to identify the novel biomarkers in glioblastoma multiforme tumors by using computational analysis

Study of the Anti-Inflammatory Mechanism of β-Carotene Based on Network Pharmacology

Potential of natural products in inflammation: biological activities, structure–activity relationships, and mechanistic targets

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