A1 Journal article – refereed

Combinatorial mutagenesis with alternative CDR-L1 and-H2 loop lengths contributes to affinity maturation of antibodies

List of Authors: Brockmann Eeva-Christine, Pyykkö Mikko, Hannula Heidi, Khan Kamran, Lamminmäki Urpo, Huovinen Tuomas

Publisher: ELSEVIER

Publication year: 2021

Journal: New Biotechnology

Journal name in source: NEW BIOTECHNOLOGY

Journal acronym: NEW BIOTECHNOL

Volume number: 60

Number of pages: 10

ISSN: 1871-6784

eISSN: 1876-4347

DOI: http://dx.doi.org/10.1016/j.nbt.2020.09.002

Loop length variation in the complementary determining regions (CDRs) 1 and 2 encoded in germline variable antibody genes provides structural diversity in naive antibody libraries. In synthetic single framework libraries the parental CDR-1 and CDR-2 length is typically unchanged and alternative lengths are provided only at CDR-3 sites. Based on an analysis of the germline repertoire and structure-solved anti-hapten and anti-peptide antibodies, we introduced combinatorial diversity with alternative loop lengths into the CDR-L1, CDR-L3 and CDR-H2 loops of anti-digoxigenin and anti-microcystin-LR single chain Fv fragments (scFvs) sharing human IGKV3-20/IGHV3-23 frameworks. The libraries were phage display selected for folding and affinity, and analysed by single clone screening and deep sequencing. Among microcystin-LR binders the most frequently encountered alternative loop lengths were one amino acid shorter (6 aa) and four amino acids longer (11 aa) CDR-L1 loops leading up to 17- and 28-fold improved affinity, respectively. Among digoxigenin binders, 2 amino acids longer (10 aa) CDR-H2 loops were strongly enriched, but affinity improved anti-digoxigenin scFvs were also encountered with 7 aa CDR-H2 and 11 aa CDR-L1 loops. Despite the fact that CDR-L3 loop length variants were not specifically enriched in selections, one clone with 22-fold improved digoxigenin binding affinity was identified containing a 2 residues longer (10 aa) CDR-L3 loop. Based on our results the IGKV3-20/IGHV3-23 scaffold tolerates loop length variation, particularly in CDR-L1 and CDR-H2 loops, without compromising antibody stability, laying the foundation for developing novel synthetic antibody libraries with loop length combinations not existing in the natural human Ig gene repertoire.

Last updated on 2021-24-06 at 10:49