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

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-kappa and Fab-lambda. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD similar to 10 -5 M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to similar 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. (c) 2022 Elsevier B.V. All rights reserved.

Automated summary

This study describes the de novo design of 9-mer peptides that bind to Fab fragments using an integrated computational and experimental approach. The designed peptides showed good affinity and high product yield, laying the groundwork for future biomanufacturing translation.