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Towards a rational design of antibody‐recruiting molecules through a computational microscopy view of their interactions with the target antibody

Annemiek Uvyn (UGent) , Corentin Tonneaux, Mathieu Fossépré, Aude Ouvrier‐Buffet, Bruno De Geest (UGent) and Mathieu Surin
(2023) CHEMISTRY-A EUROPEAN JOURNAL. 29(30).
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Abstract
Antibody recruiting molecules (ARMs) are an innovative class of chimeric molecules, consisting of an antibody-binding ligand (ABL) and a target-binding ligand (TBL). ARMs mediate ternary complex formation between a target cell of interest for elimination and endogenous antibodies that are present in human serum. Clustering of fragment crystallizable (Fc) domains on the surface of antibody-bound cells mediate destruction of the target cell by innate immune effector mechanisms. ARMs are typically designed by conjugating small molecule haptens to a (macro)molecular scaffold, without considering the structure of the respective anti-hapten antibody. Here we report on a computational molecular modeling methodology that allows for studying the close contacts between ARMs and the anti-hapten antibody, considering (1) the spacer length between ABL and TBL; (2) the number of ABL and TBL, and (3) the molecular scaffold onto which these are positioned. Our model predicts the difference in binding modes of the ternary complex and predicts which ARMs are optimal recruiters. Avidity measurements of the ARM-antibody complex and ARM-mediated antibody recruitment to cell surfaces in vitro confirmed these computational modeling predictions. This kind of multiscale molecular modelling holds potential for design of drug molecules that rely on antibody binding for their mechanism of action.
Keywords
General Chemistry, Catalysis, Organic Chemistry, antibodies, immunology, in silico, modelling, ternary complex, DYNAMICS

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Citation

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MLA
Uvyn, Annemiek, et al. “Towards a Rational Design of Antibody‐recruiting Molecules through a Computational Microscopy View of Their Interactions with the Target Antibody.” CHEMISTRY-A EUROPEAN JOURNAL, vol. 29, no. 30, 2023, doi:10.1002/chem.202300474.
APA
Uvyn, A., Tonneaux, C., Fossépré, M., Ouvrier‐Buffet, A., De Geest, B., & Surin, M. (2023). Towards a rational design of antibody‐recruiting molecules through a computational microscopy view of their interactions with the target antibody. CHEMISTRY-A EUROPEAN JOURNAL, 29(30). https://doi.org/10.1002/chem.202300474
Chicago author-date
Uvyn, Annemiek, Corentin Tonneaux, Mathieu Fossépré, Aude Ouvrier‐Buffet, Bruno De Geest, and Mathieu Surin. 2023. “Towards a Rational Design of Antibody‐recruiting Molecules through a Computational Microscopy View of Their Interactions with the Target Antibody.” CHEMISTRY-A EUROPEAN JOURNAL 29 (30). https://doi.org/10.1002/chem.202300474.
Chicago author-date (all authors)
Uvyn, Annemiek, Corentin Tonneaux, Mathieu Fossépré, Aude Ouvrier‐Buffet, Bruno De Geest, and Mathieu Surin. 2023. “Towards a Rational Design of Antibody‐recruiting Molecules through a Computational Microscopy View of Their Interactions with the Target Antibody.” CHEMISTRY-A EUROPEAN JOURNAL 29 (30). doi:10.1002/chem.202300474.
Vancouver
1.
Uvyn A, Tonneaux C, Fossépré M, Ouvrier‐Buffet A, De Geest B, Surin M. Towards a rational design of antibody‐recruiting molecules through a computational microscopy view of their interactions with the target antibody. CHEMISTRY-A EUROPEAN JOURNAL. 2023;29(30).
IEEE
[1]
A. Uvyn, C. Tonneaux, M. Fossépré, A. Ouvrier‐Buffet, B. De Geest, and M. Surin, “Towards a rational design of antibody‐recruiting molecules through a computational microscopy view of their interactions with the target antibody,” CHEMISTRY-A EUROPEAN JOURNAL, vol. 29, no. 30, 2023.
@article{01HH4EPXKXF176TT447XD52BH0,
  abstract     = {{Antibody recruiting molecules (ARMs) are an innovative class of chimeric molecules, consisting of an antibody-binding ligand (ABL) and a target-binding ligand (TBL). ARMs mediate ternary complex formation between a target cell of interest for elimination and endogenous antibodies that are present in human serum. Clustering of fragment crystallizable (Fc) domains on the surface of antibody-bound cells mediate destruction of the target cell by innate immune effector mechanisms. ARMs are typically designed by conjugating small molecule haptens to a (macro)molecular scaffold, without considering the structure of the respective anti-hapten antibody. Here we report on a computational molecular modeling methodology that allows for studying the close contacts between ARMs and the anti-hapten antibody, considering (1) the spacer length between ABL and TBL; (2) the number of ABL and TBL, and (3) the molecular scaffold onto which these are positioned. Our model predicts the difference in binding modes of the ternary complex and predicts which ARMs are optimal recruiters. Avidity measurements of the ARM-antibody complex and ARM-mediated antibody recruitment to cell surfaces in vitro confirmed these computational modeling predictions. This kind of multiscale molecular modelling holds potential for design of drug molecules that rely on antibody binding for their mechanism of action.}},
  articleno    = {{e202300474}},
  author       = {{Uvyn, Annemiek and Tonneaux, Corentin and Fossépré, Mathieu and Ouvrier‐Buffet, Aude and De Geest, Bruno and Surin, Mathieu}},
  issn         = {{0947-6539}},
  journal      = {{CHEMISTRY-A EUROPEAN JOURNAL}},
  keywords     = {{General Chemistry,Catalysis,Organic Chemistry,antibodies,immunology,in silico,modelling,ternary complex,DYNAMICS}},
  language     = {{eng}},
  number       = {{30}},
  pages        = {{15}},
  title        = {{Towards a rational design of antibody‐recruiting molecules through a computational microscopy view of their interactions with the target antibody}},
  url          = {{http://doi.org/10.1002/chem.202300474}},
  volume       = {{29}},
  year         = {{2023}},
}
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