Understanding differences between synthetic and natural antibodies can help improve antibody engineering

Anat Burkovitz, Yanay Ofran

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Synthetic libraries are a major source of human-like antibody (Ab) drug leads. To assess the similarity between natural Abs and the products of these libraries, we compared large sets of natural and synthetic Abs using “CDRs Analyzer,” a tool we introduce for structural analysis of Ab-antigen (Ag) interactions. Natural Abs, we found, recognize their Ags by combining multiple complementarity-determining regions (CDRs) to create an integrated interface. Synthetic Abs, however, rely dominantly, sometimes even exclusively on CDRH3. The increased contribution of CDRH3 to Ag binding in synthetic Abs comes with a substantial decrease in the involvement of CDRH2 and CDRH1. Furthermore, in natural Abs CDRs specialize in specific types of non-covalent interactions with the Ag. CDRH1 accounts for a significant portion of the cation-pi interactions; CDRH2 is the major source of salt-bridges and CDRH3 accounts for most hydrogen bonds. In synthetic Abs this specialization is lost, and CDRH3 becomes the main sources of all types of contacts. The reliance of synthetic Abs on CDRH3 reduces the complexity of their interaction with the Ag: More Ag residues contact only one CDR and fewer contact 3 CDRs or more. We suggest that the focus of engineering attempts on CDRH3 results in libraries enriched with variants that are not naturallike. This may affect not only Ag binding, but also Ab expression, stability and selectivity.

Original languageEnglish
Pages (from-to)278-287
Number of pages10
Issue number2
StatePublished - 1 Jan 2016

Bibliographical note

Publisher Copyright:
© 2016 Taylor & Francis Group, LLC.


  • Antibody– antigen interactions
  • Antigen binding site
  • Human-like antibodies
  • Libraries
  • Synthetic


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