Combinatorial screening of polymer nanoparticles for their ability to recognize epitopes of AAV‐neutralizing antibodies

A library of 17 nanoparticles made of acrylate and methacrylate copolymers is prepared, characterized, and screened against six epitopes of adeno‐associated viruses (AAV)‐neutralizing antibodies to assess their affinity and specificity. Peptide epitopes are immobilized onto the surface of glass beads, packed in filtration microplates, and incubated with fluorescein‐labelled nanoparticles. Following intense washing, the affinity of nanoparticles to immobilized epitopes is assessed by measuring the fluorescence of captured nanoparticles. The results show that polar monomers, acrylic acid in particular, have a positive impact on polymer affinity towards all peptides used in this study. The presence of hydrophobic monomers, on other hand, has a negative impact on polymer binding. The composition of peptides used in this study has no noticeable impact on the affinity of synthesized nanoparticles. The affinity of nanoparticles with the highest affinity to peptide targets does not exceed millimolar level. Overall, it is found that the synthesized library showed modest affinity but lacked specificity, which should be further “tuned,” for example, by using molecular imprinting to achieve an acceptable level of affinity and specificity for practical application. A small combinatorial library of polymeric nanoparticles was prepared and screened against six peptide epitopes of the variable regions of the AAV‐neutralizing antibodies following a protocol developed by the leader in this field, Prof Ken J. Shea. It addresses previously unanswered questions, particularly in relation to whether synthesized nanoparticles have not only affinity but also specificity to different peptide/protein modalities.