Mechanisms of Polymer-Antigen Binding and Hydrolysis Inhibition: Molecular Dynamics Simulations and Experimental Measurements.

In situ cancer vaccines activate antitumor immune responses by locally capturing and presenting tumor-derived antigens, in which polymers play a key role as antigen-capturing materials. However, the influence of polymer composition and degree of polymerization (DP) on antigen capture efficiency and protection mechanisms remains insufficiently understood. In this study, the tumor-specific antigen MAGE-A3, highly expressed in esophageal squamous cell carcinoma (ESCC), was employed to investigate antigen capture and stabilization by five representative polymers-chitosan, polyethyleneimine (PEI), alginate, polycaprolactone (PCL), and poly (lactic-co-glycolic acid) (PLGA)-with different DPs, using molecular dynamics simulations and in vitro experiments. All-atom simulations revealed that hydrophobic interactions dominate polymer-antigen binding, while electrostatic interactions from cationic polymers synergistically enhance binding affinity and capture efficiency. Binding free energy analysis showed that van der Waals and electrostatic contributions stabilize the complexes, whereas polar solvation partially counteracts these effects. Experimentally, low-DP chitosan exhibited the highest antigen-capture efficiency (38.9%), attributed to its small molecular size, enabling multipoint binding across the antigen surface. In contrast, high-DP polymers generated pronounced steric hindrance that suppressed antigen-enzyme interactions and inhibited hydrolysis. These findings clarify how polymer composition and chain length jointly regulate antigen capture and protection, providing mechanistic guidance for the rational design of polymer-based in situ cancer vaccines.