Unraveling the Potential Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Mechanisms of Ginger by Computational Target Fishing

Ginger (Zingiber officinale) is one of the most commonly consumed botanical foods. Owing to its anti-inflammatory and antiviral properties, ginger has been widely used as a homemade remedy during the corona virus disease 2019 (COVID-19) pandemic; however, the mechanisms of its therapeutic activities against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain obscure. In this study, we used a drug-likeness approach to screen the active compounds of ginger. Next, we identified candidate targets of active compounds responsible for the anti-SARS-CoV-2 effects of ginger using chemical similarity searching and SARS-CoV-2-human protein-protein interaction (PPI) data. Finally, we analyzed PPIs, Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment of the candidate proteins using different bioinformatics tools. A network comprising ginger compounds, human proteins, and SARS-CoV-2 proteins was built through Cytoscape 3.3. The results indicate that the anti-SARS-CoV-2 activity of ginger involves 20 active compounds, 18 potential human targets, and 12 SARS-CoV-2 proteins. These form a pharmacological network in which sigma nonopioid intracellular receptor 1 (SIGMAR1) and histone deacetylase 2 may be druggable hub proteins. In addition, molecular docking showed that 8-gingerdione and dihydrocapsaicin may preferentially interact with SIGMAR1, which was confirmed by further molecular dynamics simulation (150 ns) experiments. In conclusion, ginger targets multiple human proteins and affects multiple SARS-CoV-2 proteins to exert anti-COVID-19 effects. Although further experimental verification is needed, this study provides a quick visual overview of the anti-SARS-CoV-2 action of ginger.

Antitumor Activity and Mechanism of Robustic Acid from Dalbergia benthami Prain via Computational Target Fishing

Dalbergia benthami Prain (D.benthami) is an important legume species of the Dalbergia family, due to the use of its trunk and root heart in traditional Chinese medicine (TCM). In the present study, we reported the isolation, characterization and pharmacological activities of robustic acid (RA) from the ethyl acetate extract of D. benthami Prain. The SwissADME prediction showed that the RA satisfied the Lipinski’s rule of five (molecule weight (MW): 380.39 g/mol, lipid-water partition coefficient (log P): 3.72, hydrogen bond donors (Hdon): 1, hydrogen bond acceptors (Hacc): 6, rotatable bonds (Rbon): 3. Other chemical and pharmacological properties of this RA were also evaluated, including topological polar surface area (TPSA) = 78.13 Å and solubility (Log S) = −4.8. The probability values of the antineoplastic, anti-free radical activities and topoisomerase I (TopoI) inhibitory activity were found to be 0.784, 0.644 and 0.379, respectively. The molecular docking experiment using the Surflex-Dock showed that the Total Score and C Score of RNA binding with the human DNA-Topo I complex were 7.80 and 4. The MTS assay experiment showed that the inhibitory rates of RA on HL-60, MT4, Hela, HepG2, SK-OV-3 and MCF-7 cells were 37.37%, 97.41%, 81.22%, 34.4%, 32.68% and 51.4%, respectively. In addition, RA exhibited an inhibitory effect on the angiogenesis of zebrafish embryo, a good TopoI inhibitory activity at a 10 mM concentration and in a dose-dependent manner, excellent radical scavenging in the DPPH and ABTS assays, and the free radical scavenging rate was close to the positive control (BHT) at different concentrations (0.5–2.0 mg/mL). Furthermore, 18 potential targets were found for this RA by PharmMapper, including ANXA3, SRC, FGFR2, GSK3B, CSNK2B, YARS, LCK, EPHA2, MAPK14, RORA, CRABP2, PPP1CC, METAP2, MME, TTR, MET and KDR. The GO and KEGG pathway analysis revealed that the “protein tyrosine kinase activity”, “rap1 signaling pathway” and “PI3K-Akt signaling pathway” were significantly enriched by the RA target genes. Our results will provide new insights into the pharmaceutical use of this species. More importantly, our data will expand our understanding of the molecular mechanisms of RA functions.

Identification of the Molecular Mechanisms of Peimine in the Treatment of Cough Using Computational Target Fishing

Peimine (also known as verticine) is the major bioactive and characterized compound of Fritillariae Thunbergii Bulbus, a traditional Chinese medicine that is most frequently used to relieve a cough. Nevertheless, its molecular targets and mechanisms of action for cough are still not clear. In the present study, potential targets of peimine for cough were identified using computational target fishing combined with manual database mining. In addition, protein-protein interaction (PPI), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using, GeneMANIA and Database for Annotation, Visualization and Integrated Discovery (DAVID) databases respectively. Finally, an interaction network of drug-targets-pathways was constructed using Cytoscape. The results identified 23 potential targets of peimine associated with cough, and suggested that MAPK1, AKT1 and PPKCB may be important targets of pemine for the treatment of cough. The functional annotations of protein targets were related to the regulation of immunological and neurological function through specific biological processes and related pathways. A visual representation of the multiple targets and pathways that form a network underlying the systematic actions of peimine was generated. In summary, peimine is predicted to exert its systemic pharmacological effects on cough by targeting a network composed of multiple proteins and pathways.