De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics

ACS Chem Biol. 2024 Jul 19;19(7):1583-1592. doi: 10.1021/acschembio.4c00236. Epub 2024 Jun 25.

Abstract

The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.

MeSH terms

  • Amino Acid Sequence
  • Complementarity Determining Regions* / chemistry
  • Humans
  • Immunoglobulin Heavy Chains / chemistry
  • Models, Molecular

Substances

  • Complementarity Determining Regions
  • Immunoglobulin Heavy Chains