De novo design of a peptide ligand for specific affinity purification of human complement C1q

Affinity purification is an essential technique for isolating highly purified proteins. However, the generation of affinity ligands requires significant time and financial investment. To address these limitations, we present a novel affinity chromatography method using in silico-designed cyclic peptides as ligands. Complement C1q (C1q), a plasma protein that plays a crucial role in the classical complement pathway, was specifically selected as the target protein. AlphaFold2 was used to design specific binding cyclic peptides based on biomolecular structure prediction. The pLDDT score for the designed complex was 85.28. Based on these designs, lariat-type cyclic peptides were synthesized. They were characterized by disulfide cyclization and biotinylation, and subsequently immobilized on streptavidin carriers. The binding kinetics between C1q and the synthetic peptides were measured via surface plasmon resonance (K_D=7.79nM). Additionally, affinity column chromatography and other performance tests confirmed that the resulting column specifically captured C1q and allowed its elution from human plasma via a standard NaCl concentration gradient. Notably, the high selectivity was preserved even in the presence of plasma, thereby underscoring the practical robustness of the ligand. The purity of the purified C1q from plasma was 69.4%. By overcoming traditional constraints through (1) rapid and simple design, (2) high specificity, and (3) universal versatility without genetic modifications, this de novo design strategy represents a breakthrough in protein purification technologies.