Abstract: We designed and screened  αvβ6 polypeptide ligands with new structure by using computer-aided drug design strategy and solid-phase synthesis method,  and determined  the binding affinity between  the polypeptide ligands and αvβ6 by using enzyme-linked immunosorbent assay (ELISA) to establish a screening scheme for αvβ6 polypeptide ligands.  Firstly,  Sybyl-X 1.3 was used to perform molecular docking of the  αvβ6 polypeptide ligands and natural ligands. Secondly, Amber 16 was used to perform molecular dynamics simulation to determine the binding mode between the polypeptide ligands and αvβ6 protein,  and RGDLXXL (X was any amino acid) was used as the core structure of the polypeptide ligand, the virtual peptide library was constructed by gradual extension of amino acids,  polypeptide ligands with a length of 7—10 amino acids were screened， and new polypeptide ligands different from the core of RGDLXXL were designed and screened by similar amino acid substitution method. Finally,  the newly designed polypeptide ligands were synthesized by solid-phase synthesis method, and  the binding affinity of polypeptide ligand-αvβ6 was determined by indirect ELISA method.   The molecular docking and molecular dynamics simulation results of polypeptide ligands and natural ligands show that the binding of αvβ6 to the ligand is mainly achieved through the hydrogen bond formation between Asp218 and the polypeptide ligand,  and the metal chelation between Mg²⁺ and the polypeptide ligand. Combined with virtual combination screening and similar amino acid substitution,  we find that polypeptides such as GRTDLGTLLFR，GRRTDLATIHG，RTDVGRVRGRG and RGDVGRVGR all meet this binding pattern, and  the affinity between  RTDVGRVRGRG and αvβ6 is 10.76 μmol/L. Therefore,  RTDVGRVRGRG  and αvβ6  have a good affinity and are a new   αvβ6 polypeptide ligand.

Key words: integrin αvβ6,  , polypeptide,  , drug design,  , affinity,  , enzyme-linked immunosorbent assay (ELISA)