Network pharmacology, computational biology integrated surface plasmon resonance technology reveals the mechanism of ellagic acid against rotavirus

• Published in: Scientific reports 2024-03, Vol.14 (1), p.7548-7548, Article 7548
• Main Authors: Zheng, Jiangang, Haseeb, Abdul, Wang, Ziyang, Wang, Hejie
• Format: Article
• Language: English
• Subjects: 631/114; 631/154; 631/45; Acids; Albumins; Computational Biology; Computer applications; Crystal structure; Cytokines; Drugs, Chinese Herbal; Ellagic acid; Ellagic Acid - pharmacology; Enteritis; Epidermal Growth Factor; Free energy; Humanities and Social Sciences; IL-1β; Interleukin 4; MAP kinase; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular dynamics simulation; multidisciplinary; Network Pharmacology; NF-κB protein; p53 Protein; Pharmacology; Proteins; Resonance; Rotavirus; Saturation mutagenesis; Saturation mutation analysis; Science; Science (multidisciplinary); Signal transduction; Smad protein; Software; Surface Plasmon Resonance; TLR4 protein; Toll-Like Receptor 4; Toll-like receptors; Tumor Necrosis Factor-alpha; Tumor necrosis factor-TNF; Tumor necrosis factor-α; Viruses
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-58301-6

The target and mechanism of ellagic acid (EA) against rotavirus (RV) were investigated by network pharmacology, computational biology, and surface plasmon resonance verification. The target of EA was obtained from 11 databases such as HIT and TCMSP, and RV-related targets were obtained from the Gene Cards database. The relevant targets were imported into the Venny platform to draw a Venn diagram, and their intersections were visualized. The protein–protein interaction networks (PPI) were constructed using STRING, DAVID database, and Cytoscape software, and key targets were screened. The target was enriched by Gene Ontology (GO) and KEGG pathway, and the ‘EA anti-RV target-pathway network’ was constructed. Schrodinger Maestro 13.5 software was used for molecular docking to determine the binding free energy and binding mode of ellagic acid and target protein. The Desmond program was used for molecular dynamics simulation. Saturation mutagenesis analysis was performed using Schrodinger's Maestro 13.5 software. Finally, the affinity between ellagic acid and TLR4 protein was investigated by surface plasmon resonance (SPR) experiments. The results of network pharmacological analysis showed that there were 35 intersection proteins, among which Interleukin-1β (IL-1β), Albumin (ALB), Nuclear factor kappa-B1 (NF-κB1), Toll-Like Receptor 4 (TLR4), Tumor necrosis factor alpha (TNF-α), Tumor protein p53 (TP53), Recombinant SMAD family member 3 (SAMD3), Epidermal growth factor (EGF) and Interleukin-4 (IL-4) were potential core targets of EA anti-RV. The GO analysis consists of biological processes (BP), cellular components (CC), and molecular functions (MF). The KEGG pathways with the highest gene count were mainly related to enteritis, cancer, IL-17 signaling pathway, and MAPK signaling pathway. Based on the crystal structure of key targets, the complex structure models of TP53-EA, TLR4-EA, TNF-EA, IL-1β-EA, ALB-EA, NF-κB1-EA, SAMD3-EA, EGF-EA, and IL-4-EA were constructed by molecular docking (XP mode of flexible docking). The MMGBS analysis and molecular dynamics simulation were also studied. The Δaffinity of TP53 was highest in 220 (CYS → TRP), 220 (CYS → TYR), and 220 (CYS → PHE), respectively. The Δaffinity of TLR4 was highest in 136 (THR → TYR), 136 (THR → PHE), and 136 (THR → TRP). The Δaffinity of TNF-α was highest in 150 (VAL → TRP), 18 (ALA → GLU), and 144 (PHE → GLY). SPR results showed that ellagic acid could bind TLR4 protein specifically. TP53, TLR4, and