Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies
Aliza Borenstein-Katz1, Shira Warszawski2, Ron Amon3
1Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
Abstract:
Glycans decorate the cell surface, secreted glycoproteins and glycolipids, and altered glycans are often found in cancers. Despite their high diagnostic and therapeutic potential, however, glycans are polar and flexible molecules that are quite challenging for the development and design of high-affinity binding antibodies. To understand the mechanisms by which glycan neoantigens are specifically recognized by antibodies, we analyze the biomolecular recognition of the tumor-associated carbohydrate antigen CA19-9 by two distinct antibodies using X-ray crystallography. Despite the potential plasticity of glycans and the very different antigen-binding surfaces presented by the antibodies, both structures reveal an essentially identical extended CA19-9 conformer, suggesting that this conformer's stability selects the antibodies. Starting from the bound structure of one of the antibodies, we use the AbLIFT computational algorithm to design a variant with seven core mutations in the variable domain's light-heavy chain interface that exhibits tenfold improved affinity for CA19-9. The results reveal strategies used by antibodies to specifically recognize glycan antigens and show how automated antibody-optimization methods may be used to enhance the clinical potential of existing antibodies.
Insights
Researchers studied how antibodies recognize cancer-associated carbohydrate antigen CA19-9. They found a stable glycan form selects antibodies and used computational design to improve antibody affinity tenfold for potential cancer diagnostics and therapeutics.
Area of Science:
- Biochemistry
- Structural Biology
- Immunology
Background:
- Glycans on cell surfaces are crucial in biological processes, and their alterations are common in cancer.
- Developing high-affinity antibodies for flexible, polar glycan antigens presents significant challenges.
- Tumor-associated carbohydrate antigen CA19-9 is a key biomarker in certain cancers.
Purpose of the Study:
- To elucidate the molecular mechanisms of antibody recognition for glycan neoantigens, specifically CA19-9.
- To investigate the structural basis of antibody-glycan interactions.
- To explore computational methods for enhancing antibody affinity to cancer biomarkers.
Main Methods:
- X-ray crystallography was employed to analyze the complex of CA19-9 with two distinct antibodies.
- Structural analysis focused on the binding interface and glycan conformation.
- The AbLIFT computational algorithm was used to design antibody variants with improved affinity.
Main Results:
- Both antibodies recognized an essentially identical extended conformer of CA19-9, suggesting conformational selection.
- The stability of this CA19-9 conformer appears to be a key factor in antibody binding.
- A computationally designed antibody variant showed a tenfold increase in affinity for CA19-9.
Conclusions:
- Antibody binding to glycan antigens is influenced by the inherent stability of specific glycan conformations.
- Computational antibody design strategies, like AbLIFT, can significantly enhance binding affinity.
- Optimized antibodies targeting cancer-associated glycans hold promise for improved diagnostics and therapeutics.
