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

Affinity purification is a essential technique for isolating highly purified proteins; however, generating affinity ligands require significant time and financial investment. To address these limitations, this study proposes a novel affinity chromatography method utilizing in silico-designed cyclic peptides as ligands. Targeting Complement C1q (C1q), a plasma protein that plays crucial roles in classical complement pathway, we employed the biomolecular structure prediction model, AlphaFold2, to design specific binding cyclic peptides. Based on these designs, we synthesized lariat-type cyclic peptides characterized by disulfide cyclization and biotinylation, which were subsequently immobilized on streptavidin carriers. Performance tests confirmed that the resulting column specifically captured C1q, allowing for elution via a standard NaCl concentration gradient. Notably, high selectivity was preserved even in the presence of plasma, underscoring the ligands practical robustness. By overcoming traditional constraints through (1) rapid and simple design, (2) high specificity, and (3) universal versatility without genetic modification, this de novo design strategy represents a potential breakthrough in protein purification technologies. HighlightsO_LIAI-driven de novo design generated a specific cyclic peptide ligand for Complement C1q C_LIO_LIThe synthetic ligand enabled one-step purification of Complement C1q directly from human plasma C_LIO_LIMild elution conditions preserved the targets oligomeric structure and native interactome C_LIO_LIThis label-free strategy offers a rapid, low-cost alternative to antibody-based chromatography C_LI