Ultrasound-Assisted Synthesis, Spectroscopic Characterization, and Molecular Docking of Novel Benzo[g]pterin-Based Pyrimidine Derivatives against Human Thymidylate Synthase

Abstract

A novel series of nitrogen-rich heterocyclic derivatives incorporating a fused benzo[g]pterin scaffold expanded with functionalized pyrimidine, pyrimidinone, pyrimidinethione, aminopyrimidine, and cyano-substituted motifs was designed and efficiently synthesized via ultrasound-assisted convergent routes. Using 2-aminobenzo[g]pteridin-4-one as a key synthon, three distinct synthetic pathways were established using activated methylene reagents (malononitrile or ethyl cyanoacetate), aromatic aldehydes, and various binucleophiles under acoustic cavitation. The target products (H1-H5 and K1–K6) were obtained in good to excellent isolated yields (60%–85%). Their chemical structures were unambiguously confirmed by FTIR, 1H-NMR, and 13C-NMR spectroscopic techniques. To evaluate their potential as targeted antitumor agents, representative derivatives spanning the synthetic series were subjected to molecular docking against human thymidylate synthase (hTS, PDB ID: 6QXG) and compared with the standard clinical antimetabolite 5-fluorouracil (5-FU). Among the evaluated compounds, derivative H1 exhibited an outstanding binding affinity (ΔG = -8.2 kcal/mol), significantly outperforming 5-FU (ΔG = -4.3 kcal/mol), H5 (ΔG = -4.4 kcal/mol), and K4 (ΔG = -3.8 kcal/mol). Detailed protein–ligand interaction profiling revealed that H1 accommodated precisely within the canonical catalytic pocket of hTS, forming key non-covalent interactions with crucial catalytic and binding-site residues, including Cys195, Asp218, Tyr258, Arg50, Arg215, Ser216, His256, and the intersubunit basic catalytic clamp Arg175/Arg176. These findings highlight the efficiency of the ultrasound-promoted synthetic protocols and position compound H1 as a highly promising hit structure for further biochemical and targeted anticancer evaluation.