Rational design of a small peptidomimetic ligand to capture a viral spike protein

• A novel synthetic peptidomimetic was designed to bind the SARS-CoV-2 spike protein. • Virtual and experimental screening methods were combined to select the lead ligand. • The affinity ligand was efficient in capturing and recovering the target protein. • Molecular simulations predicted the binding site in highly accessible RBD region. • Lead adsorbents bound > 95 % of spike proteins, with 64–73 % recovery, and a 15 enrichment factor. The availability of purified antigenic proteins is critical to develop agents to prevent, diagnose, or treat infectious diseases. In this context, antigenic proteins are produced by recombinant expression in host cells and further purified, typically by chromatographic methods. Chromatographic steps that allow the one-step capture of the antigenic protein are important to streamline the purification train. Here, we present the design and development of an adsorbent bearing a synthetic affinity ligand to capture the SARS-CoV-2 spike protein, used as a model antigenic protein. A 120-ligand combinatorial library was designed in silico and then synthesised in solid phase, and both were computationally and experimentally screened for binding to the spike protein. One lead ligand was selected for yielding > 95 % binding, and 64–73 % recovery of original strain spike protein, its receptor-binding domain (RBD), and Omicron BA.5 variant spike protein. An enrichment factor of 15 was found when capturing the spike protein from a clarified supernatant sample. Complementary molecular dynamics simulations allowed a better understanding of the interactions between the lead ligand and the spike protein, which mainly consist of hydrophobic interactions, some hydrogen bonds and salt bridges formed with an important ligand carboxyl group. Overall, the methodology is a fast and efficient platform to develop affinity ligands for the purification of antigenic proteins in future pandemics.