Discovery of a broad-spectrum affibody ligand for COVID-19 vaccine purification

The coronavirus disease 2019 (COVID-19) pandemic has posed not only a severe threat to human health and the global economy but also greater requirements for the efficient isolation of highly variable viruses. To address this dilemma, a strategy for the development of affibody ligands targeting the conserved region of the receptor binding domain (RBD) on the spike (S) protein was proposed, and a virtual affibody library (148 molecules) was constructed on the basis of key residue identification of the 3-2A2-4 nanobody that binds to the RBD. The most potential candidate, Q30, was obtained after two rounds of docking and molecular dynamics (MD) simulations. Competitive ELISA confirmed that Q30 bound to the conserved region of the RBD, rather than to the human angiotensin-converting enzyme 2-binding region. Furthermore, Q30 had high affinities of 0.23 μmol/L for the wild-type RBD and 0.81 μmol/L for the Omicron variant, indicating good broad-spectrum affinity. By coupling Q30 onto Sepharose Fast Flow (SepFF), the affinity gel (Q30-SepFF) could efficiently adsorb both the RBD and its Omicron variant, validating the broad-spectrum of the chromatography. Affinity chromatography was successfully applied for the purification of the RBD (a purity of 87.52 %), the RBD omicron variant (a purity of 89.41 %) and the Omicron vaccine (a purity of 84.62 %), indicating great applicability in vaccine purification.