A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen

Ron Amon, Oliver C. Grant, Shani Leviatan Ben-Arye, Spandana Makeneni, Anita K. Nivedha, Tal Marshanski, Christoffer Norn, Hai Yu, John N. Glushka, Sarel J. Fleishman, Xi Chen, Robert J. Woods, Vered Padler-Karavani

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Abstract

Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the antibody combining site were identified by site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates.

LanguageEnglish (US)
Article number10786
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Tumor-Associated Carbohydrate Antigens
Polysaccharides
Antibodies
Screening
Monoclonal Antibodies
Carbohydrates
Mutagenesis
Microarrays
Molecular dynamics
Binding Sites
Throughput
Nuclear magnetic resonance
Antigens
Computer simulation

ASJC Scopus subject areas

  • General

Cite this

Amon, R., Grant, O. C., Leviatan Ben-Arye, S., Makeneni, S., Nivedha, A. K., Marshanski, T., ... Padler-Karavani, V. (2018). A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. Scientific Reports, 8(1), [10786]. https://doi.org/10.1038/s41598-018-29209-9

A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. / Amon, Ron; Grant, Oliver C.; Leviatan Ben-Arye, Shani; Makeneni, Spandana; Nivedha, Anita K.; Marshanski, Tal; Norn, Christoffer; Yu, Hai; Glushka, John N.; Fleishman, Sarel J.; Chen, Xi; Woods, Robert J.; Padler-Karavani, Vered.

In: Scientific Reports, Vol. 8, No. 1, 10786, 01.12.2018.

Research output: Contribution to journalArticle

Amon, R, Grant, OC, Leviatan Ben-Arye, S, Makeneni, S, Nivedha, AK, Marshanski, T, Norn, C, Yu, H, Glushka, JN, Fleishman, SJ, Chen, X, Woods, RJ & Padler-Karavani, V 2018, 'A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen' Scientific Reports, vol. 8, no. 1, 10786. https://doi.org/10.1038/s41598-018-29209-9
Amon, Ron ; Grant, Oliver C. ; Leviatan Ben-Arye, Shani ; Makeneni, Spandana ; Nivedha, Anita K. ; Marshanski, Tal ; Norn, Christoffer ; Yu, Hai ; Glushka, John N. ; Fleishman, Sarel J. ; Chen, Xi ; Woods, Robert J. ; Padler-Karavani, Vered. / A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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