Mechanistic Insights into Usnic Acid Derivatives for Gut Inflammation in Colon Cancer: An In-Silico and Systems Biology Study

Abstract

Colon cancer (CC) is a major global health concern, accounting for approximately 930,000 deaths in 2020. Chronic intestinal inflammation contributes to CC development by promoting genetic instability, dysregulated signaling, and malignant transformation of colonic epithelial cells. In this study, we explored natural Usnic Acid (UA) derivatives as potential modulators of inflammation-associated pathways in CC using in-silico approaches. A combination of molecular docking, molecular dynamics (MD) simulations, principal component analysis (PCA), Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations, and network pharmacology analyses was applied. Among the screened derivatives, Usimine A (USA) exhibited the highest predicted binding affinity (-6.20 kcal/mol) relative to the reference compound 5-Fluorouracil (-5.13 kcal/mol), forming stable interactions with key residues, including a hydrogen bond with Ser530 and a C-H bond with Ser353. MD simulations indicated stable protein-ligand interactions for USA, supported by analyses of RMSD, RMSF, radius of gyration, solvent-accessible surface area, PCA, and dynamic cross-correlation. MM/GBSA analysis predicted a favorable binding free energy for USA (-59.97 ± 5.84 kcal/mol) compared to 5-Fluorouracil (-14.21 ± 1.67 kcal/mol). Network pharmacology and pathway enrichment (GO and KEGG) analyses identified multiple inflammation- and cancer-related pathways, with the HIF-1 signaling pathway (hsa04066) prominently highlighted. This pathway serves as a key regulator linking cellular hypoxia to inflammatory responses and may underlie USA's potential anti-inflammatory effects. These computational results provide mechanistic insights into UA derivatives and suggest candidates for further experimental evaluation in inflammation-associated CC.