Protein–protein interaction (PPI) and molecular docking study

A protein–protein interaction (PPI) network of the twenty selected targets of XNT was directly constructed via cytoscape integrated STRING database (https://string-db.org/) with cutoff score 0.4 and maximum additional interaction of 5^52,54,55. Subsequently, on the established PPI network, CytoHubba and MCODE (the Molecular Complex Detection) plugins of cystoscope were applied. The cytoHubba plugin constructed the network based on the highest degree of neighborhood algorithm from the PPI network. The values for MCODE analysis were set as degree cutoff score; 2, node cutoff score; 0.2, K-core value; 2 and maximum depth; 100.

Furthermore, to validate the ligand–protein interaction which was exhibited by PharmMapper and DRAR-CPI server, molecular docking study was performed. The ligand (XNT) SDF file was acquired from PubChem (CID: 93,135) and PDB files of two randomly selected proteins from the MCODE predicted results were retrieved from Protein Data Bank (https://www.rcsb.org)⁵⁶. The ligand and protein files were prepared through BIOVIA Discovery Studio Visualizer version 20.1.0 software and Autodock Vina docking was executed by using PyRx biological software v 0.8 (https://pyrx.sourceforge.io/)^57,58. The visualization of docking results was performed by Discovery Studio Visualizer.