Network pharmacology, computational biology integrated surface plasmon resonance technology reveals the mechanism of salidroside in alleviating diabetic amyotrophy

Abstract

Objective To explore the target and mechanism of Salidroside (SDS) in the treatment of Diabetic amyotrophy (DPN) employing network pharmacology, computational biology, and surface plasmon resonance verification. Method: The target associated with SDS was acquired from the ChEmBL database and DPN-related targets were obtained from the GeneCards database. Relevant targets were imported into the Venny platform to generate a Venn diagram, and their intersections were visualized. The target protein-protein interaction (PPI) network was constructed using STRING, DAVID database, and Cytoscape software, and core targets were screened. After subjecting the targets to GO enrichment and KEGG pathway analysis, a network "target-pathway for SDS in alleviating DPN" was set up. The Schrodinger Maestro 13.5 software was utilized for molecular docking in order to ascertain the binding free energy and binding mode between SDS and target proteins. Molecular dynamics simulations were performed using the Desmond program. Saturation mutation analysis was performed using Schrodinger's Maestro 13.5 software. Finally, SPR technology was used to explore the affinity between SDS and Caspase3 protein. Results Network pharmacological analysis showed that there was a total of 61 intersection proteins, among which TNF, APP, Caspase3, PPARG, NQO1, HDAC1, BCL2, SRC, HDAC6, ACE, MAPK3, HSP90AA1, ATM, and REN were potential core targets for SDS to alleviate DPN. The enrichment analysis of GO function and KEGG pathways revealed that the targets primarily participated in diverse biological processes, cellular components alteraions, and molecular functions associated with apoptosis, neurons and transmitters, as well as metabolic pathways involved in lipid and atherosclerosis, apoptosis, and neurodegenerative pathways. Based on the crystal structure of the potential core protein, the complex structure model of the core target-SDS was created using molecular docking (XP mode of flexible docking), and the MMGBS analysis was carried out. Finally, the molecular dynamics simulation was carried out. The Δaffinity of Caspase3 was highest in 206 (TRP→GLY), 206 (TRP→LYS), and 206 (TRP→ALA). The corresponding values were 10.847 kcal/mol, 10.008 kcal/mol, and 9.725 kcal/mol. The SPR results data demonstrated specific binding and kinetic compatibility between the SDS and Caspase3 proteins. Conclusion Caspase3 is a potential target for SDS to alleviate DPN which may eventually play a role in alleviating DPN by regulating apoptosis-related pathways and providing a theoretical basis along with clues for the research and development of SDS as anti-alleviating DPN drugs.