Nigellidine from Nigella sativa Targets AKT1 and GAPDH in rectal cancer: Insights from network pharmacology and molecular dynamics simulations

Rectal cancer remains a global clinical challenge. We applied an integrated network-pharmacology and molecular simulation pipeline to prioritize Nigella sativa phytochemicals against rectal cancer. From an initial database/literature collection (≈110-120 compounds) we filtered 10 bioactive phytochemicals by DL (≥0.18) and OB (≥30%). Target prediction for these 10 compounds returned ~1,190 candidate targets; intersecting these with rectal-cancer associated genes yielded 183 common targets that were used to construct the compound-target-pathway network. Topological analysis identified ALB, AKT1, GAPDH, and IL6 as hub proteins. Survival and expression analyses revealed that ALB expression was significantly associated with disease-free survival (DFS; log-rank p = 0.03). Molecular docking of the top compounds against the four hubs showed Nigellidine as the best binder (AKT1: -11.1 kcal·mol⁻¹; GAPDH: -8.4 kcal·mol - ¹). Nigellidine complexes were subjected to 150 ns molecular dynamics simulations (3,000 frames saved at 50 ps intervals): GAPDH-Nigellidine displayed RMSD stabilization mostly around ~8.0 Å with a brief transient peak (~40-64 Å) due to conformational shift and got stables afterwards. And the AKT1-Nigellidine complex remained mostly within ~1.2-2.4 Å, indicating sustained conformational stability. Hydrogen-bond occupancy averaged ~1-2 bonds during the trajectories. MM-GBSA analysis further supported preferential binding to GAPDH (ΔGbind ≈ -85.28 kcal·mol⁻¹) versus AKT1 (ΔGbind ≈ -24.09 kcal·mol⁻¹). Pathway enrichment implicated PI3K-AKT, HIF-1 and inflammatory signaling as major affected pathways. Taken together, our in-silico results nominate Nigellidine as a prioritized multi-target candidate that may modulate oncogenic signaling (AKT1 and GAPDH). These findings provide a quantitative, systems-level rationale for targeted experimental validation of N. sativa phytochemicals in rectal cancer.