ABSTRACT
The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.
ABSTRACT
Purpose Pulmonary fibrosis caused by COVID-19 pneumonia is a serious complication of COVID-19 infection, there is a lack of effective treatment methods clinically. This article explored the mechanism of action of berberine in the treatment of COVID-19 (Corona Virus Disease 2019, COVID-19) pneumonia pulmonary fibrosis with the help of the network pharmacology and molecular docking. Methods We predicted the role of berberine protein targets with the Pharmmapper database and the 3D structure of berberine in the Pubchem database. And GeneCards database was used in order to search disease target genes and screen common target genes. Then we used STRING web to construct PPI interaction network of common target protein. The common target genes were analyzed by GO and KEGG by DAVID database. The disease-core target gene-drug network was established and molecular docking was used for prediction. We also analyzed the binding free energy and simulates molecular dynamics of complexes. Results Berberine had 250 gene targets, COVID-19 pneumonia pulmonary fibrosis had 191 gene targets, the intersection of which was 23 in common gene targets. Molecular docking showed that berberine was associated with CCl2, IL-6, STAT3 and TNF-α. GO and KEGG analysis reveals that berberine mainly plays a vital role by the signaling pathways of influenza, inflammation and immune response. Conclusion Berberine acts on TNF-α, STAT3, IL-6, CCL2 and other targets to inhibit inflammation and the activation of fibrocytes to achieve the purpose of treating COVID-19 pneumonia pulmonary fibrosis.
ABSTRACT
The coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is ongoing. Individuals with sarcoidosis tend to develop severe COVID-19; however, the underlying pathological mechanisms remain elusive. To determine common transcriptional signatures and pathways between sarcoidosis and COVID-19, we investigated the whole-genome transcriptome of peripheral blood mononuclear cells (PBMCs) from patients with COVID-19 and sarcoidosis and conducted bioinformatic analysis, including gene ontology and pathway enrichment, protein-protein interaction (PPI) network, and gene regulatory network (GRN) construction. We identified 33 abnormally expressed genes that were common between COVID-19 and sarcoidosis. Functional enrichment analysis showed that these differentially expressed genes were associated with cytokine production involved in the immune response and T cell cytokine production. We identified several hub genes from the PPI network encoded by the common genes. These hub genes have high diagnostic potential for COVID-19 and sarcoidosis and can be potential biomarkers. Moreover, GRN analysis identified important microRNAs and transcription factors that regulate the common genes. This study provides a novel characterization of the transcriptional signatures and biological processes commonly dysregulated in sarcoidosis and COVID-19 and identified several critical regulators and biomarkers. This study highlights a potential pathological association between COVID-19 and sarcoidosis, establishing a theoretical basis for future clinical trials.
ABSTRACT
INTRODUCTION: Zukamu granules may play a potential role in the fight against the Coronavirus, COVID-19. The purpose of this study was to explore the mechanisms of Zukamu granules using network pharmacology combined with molecular docking. METHODS: The Traditional Chinese Medicine systems pharmacology (TCMSP) database was used to filter the active compounds and the targets of each drug in the prescription. The Genecards and OMIM databases were used for identifying the targets related to COVID-19. The STRING database was used to analyze the intersection targets. Compound - target interaction and protein-protein interaction networks were constructed using Cytoscape to decipher the anti-COVID-19 mechanisms of action of the prescription. The Kyoto Encyclopedia of Genes and Genome (KEGG) pathway and Gene Ontology (GO) enrichment analysis was performed to investigate the molecular mechanisms of action. Finally, the interaction between the targets and the active compounds was verified by molecular docking technology. RESULTS: A total of 66 targets were identified. Further analysis identified 10 most important targets and 12 key compounds. Besides, 1340 biological processes, 43 cell compositions, and 87 molecular function items were obtained (P < 0.05). One hundred and thirty pathways were obtained (P < 0.05). The results of molecular docking showed that there was a stable binding between the active compounds and the targets. CONCLUSION: Analysis of the constructed pharmacological network results allowed for the prediction and interpretation of the multi-constituent, multi-targeted, and multi-pathway mechanisms of Zukamu granules as a potential source for supportive treatment of COVID-19.