Designing & screening of siRNA molecules for silencing the impact of the VEGF gene in cancer cells

Cancer is a complex disease characterized by uncontrolled cell proliferation and metastasis, with breast cancer remaining a leading cause of mortality among women worldwide. Hypoxia-inducible factor (HIF) and vascular endothelial growth factor (VEGF) are key mediators of angiogenesis, sustaining tumor growth and progression. RNA interference (RNAi) has emerged as a promising gene-silencing strategy for targeted cancer therapy. In this study, we designed small interfering RNAs (siRNAs) against VEGF mRNA using computational approaches. VEGF gene sequences were retrieved from NCBI, and siRNAs were designed using siDirect v2.0 and i-Score Designer. Candidate siRNAs were screened based on GC content (30–52 %), secondary structure, and thermodynamic stability. Hybridization energy analysis revealed favourable binding to VEGF mRNA, ranging from –31.1 to –37.3 kcal/mol. Molecular docking with h-Argonaute-2 (h-Ago2) yielded docking scores between –330 and –351 kcal/mol, indicating efficient RISC loading. Molecular dynamics (MD) simulations further demonstrated stable siRNA–Ago2 complexes, with RMSD values stabilizing around 2.1–2.6 Å and RMSF fluctuations primarily localized to the PAZ and MID domains. These findings confirm strong binding affinity, structural stability, and specificity of the designed siRNAs. Overall, our results suggest that RNAi-based silencing of VEGF holds significant potential as a therapeutic strategy for inhibiting angiogenesis in breast cancer.