iRGD-functionalized PLGA nanocomplex co-loaded with paclitaxel and Trametes robiniophila Murr for targeted inhibition of chemoresistant and metastatic signaling gene PDCD4 in colon cancer.

Metastasis and chemoresistance remain key challenges in colon tumor management. Integrating transcriptomic screening with molecular modeling may reveal actionable therapeutic targets for rational nanocomplex design. Transcriptomic datasets GSE44076 (n = 98) and GSE253699 (n = 6) were analyzed using limma (adjusted p < 0.05, |log₂FC| > 1). Differentially expressed genes were intersected with curated metastasis and chemoresistance panels which resulted in 18 overlapping targets. Hub genes were identified via STRING and Cytoscape-BiNGO, and prognostic analysis using KMplotter highlighted PDCD4 and CCND1 as favorable markers. A PTX-TP@PLGA-iRGD nanocomplex was designed by co-encapsulating paclitaxel and Trametes robiniophila Murr-derived metabolites within a PLGA matrix functionalized with iRGD. Nanocomplexes were characterized by dynamic light scattering, zeta potential, and HPLC for size, stability, and drug encapsulation. Functional validation included docking, 50 ns MD simulations, in vitro cytotoxicity uptake, and target engagement assays. PDCD4 and CCND1 emerged as convergence nodes, with PDCD4 showing stage-wise downregulation (p = 0.014) and positive correlation with immune infiltration. The nanocomplex exhibited a uniform particle size (~ 165 nm, PDI 0.12), and encapsulation efficiency > 75%. In vitro, PTX-TP@PLGA-iRGD demonstrated superior cytotoxicity (IC₅₀ ≈ 4.5 nM in HCT116; 6.5 nM in HT-29) compared to PTX-TP@PLGA and free PTX. Cellular uptake increased ~ 2.8-2.9× with iRGD modification, confirming receptor-mediated endocytosis. Clonogenic assays showed the lowest surviving fraction (~ 22-28%), and PDCD4 expression was upregulated (~ 2.2-fold HCT116; ~1.9-fold HT-29) following treatment. Docking revealed strong PDCD4-ligand affinities (- 6.0 to - 9.6 kcal/mol), and MD trajectories were stable (RMSD 4-6.5 Å; Rg 25-26.5 Å). The study identifies PDCD4 as a key therapeutic target and demonstrates that the PTX-TP@PLGA-iRGD nanocomplex enhances drug potency, selectivity and molecular engagement. This study offers a promising strategy to overcome metastasis and chemoresistance in colon cancer. Not applicable.