Fig. 5

Identification and prediction of active compounds of GMK and their DNA methyltransferase targets. (A) Workflow of compound selection from GMK. (B) Venn diagram of target overlap between PubChem and ChEMBL. (C) Bar graph showing the number of target genes associated with each active compound in GMK. (D) Network diagram of active molecules and herbal components constructed to target DNA methyltransferases. (E) Predicted protein structures of DNMT1 analyzed with AlphaFold3 algorithm, with high-ranking scores of 0.75. (F) Molecular docking of Quercetin and Genistein with DNMT1. Top: Quercetin–DNMT1; bottom: Genistein–DNMT1. Left panels show 3D binding poses; right panels depict 2D interaction maps with key residues (chain A numbering). Ligands are shown as sticks and colored by atom type: C (dark gray/black), O (red), N (blue), H (white), S (yellow). DNMT1 is rendered as a cartoon colored by secondary structure: α-helix (red), β-sheet (cyan), turns/bends (green), coils/loops (gray). Interaction legend (right panels): van der Waals (green dotted), conventional H-bond (light-green dashed), C–H bond (dark-green dashed), π–π T-shaped (pink dashed), π–alkyl (purple dashed), π–sulfur (yellow dashed), unfavorable contacts including bump or acceptor–acceptor clash (red dashed).