Abstract:The molecular mechanism for the binding sites, driving forces and the interaction intensity between sialyltransferase (ST) and soyasaponin I was investigated by molecular docking and free energy calculation based on the crystal structure. The van der Waals force and electrostatic interaction were considered as the main driving forces, while polar solvation energy behaved in an opposite manner. The hydrophobic interaction was formed between soyasaponin I and eight amino acid residues, i.e., Gly149, Ser151, Met172, Asn173, Phe292, Trp300, His301, and Ser325. Hydrogen bonding was found between soyasaponin I and eleven amino acid residues, including Asn150, Tyr194, Ser271, Thr272, Gly273, Ile274, Gly291, Gly293, His302, Glu305, and Glu324. Soyasaponin I was a competitive inhibitor which occupied 11 of the 12 amino acid residues that accommodated the substrate CMP-β-N-acetylneuramic acid. These results provide a theoretical basis for the development and utilization of soyasaponin I as a ST inhibitor.
