De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G

• Published in: Journal of Chromatography A 2022-04, Vol.1669, p.462941, Article 462941
• Main Authors: Xiao, Xingqing, Kilgore, Ryan, Sarma, Sudeep, Chu, Wenning, Menegatti, Stefano, Hall, Carol K.
• Format: Article
• Language: English
• Subjects: Affinity ligands; Biorecognition; Fragment antigen binding; Ligand design; Protein chromatography
• ISSN: 0021-9673
• DOI: 10.1016/j.chroma.2022.462941

•Computational protocol to discover peptide ligands that capture Fab-κ and λ.•Five peptides identified via our in-house PepBD algorithm and atomistic MD simulations.•Binding capacities up to 32 mg Fab per mL resin and mild Fab binding affinity (KD ∼ 10−5 M).•Dynamic studies returned product yield up to ∼90%.•Lays groundwork for future development of biomanufacturing ligands. Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD ∼ 10−5 M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to ∼90%. Preliminary purification studies provided purities of 83–93% and yields of 11–89%. These results lay the groundwork for future development of these ligands towards biomanufacturing translation.