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Cited by 103

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Accurate de novo design of high-affinity protein-binding macrocycles using deep learning

Rettie, Stephen A., Juergens, David, Adebomi, Victor, Bueso, Yensi Flores, Zhao, Qinqin, Leveille, Alexandria N., Liu, Andi, Bera, Asim K., Wilms, Joana A., Üffing, Alina, Kang, Alex, Brackenbrough, Evans, Lamb, Mila, Gerben, Stacey R., Murray, Analisa, Levine, Paul M., Schneider, Maika, Vasireddy, Vibha, Ovchinnikov, Sergey, Weiergräber, Oliver H., Willbold, Dieter, Kritzer, Joshua A., Mougous, Joseph D., Baker, David, DiMaio, Frank, Bhardwaj, Gaurav·2025·Nature Chemical Biology
DOI 10.1038/s41589-025-01929-w
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Abstract

Developing macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic binders against protein targets of interest. We tested 20 or fewer designed macrocycles against each of four diverse proteins and obtained binders with medium to high affinity against all targets. For one of the targets, Rhombotarget A (RbtA), we designed a high-affinity binder ( K d < 10 nM) despite starting from the predicted target structure. X-ray structures for macrocycle-bound myeloid cell leukemia 1, γ-aminobutyric acid type A receptor-associated protein and RbtA complexes match closely with the computational models, with a Cα root-mean-square deviation < 1.5 Å to the design models. RFpeptides provides a framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.

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Metadata

Authors
Rettie, S. A., Juergens, D., Adebomi, V., Bueso, Y. F., Zhao, Q., Leveille, A. N., Liu, A., Bera, A. K., Wilms, J. A., Üffing, A., Kang, A., Brackenbrough, E., Lamb, M., Gerben, S. R., Murray, A., Levine, P. M., Schneider, M., Vasireddy, V., Ovchinnikov, S., Weiergräber, O. H., Willbold, D., Kritzer, J. A., Mougous, J. D., Baker, D., DiMaio, F., & Bhardwaj, G.
Venue
Nature Chemical Biology
Publisher
Springer Science and Business Media LLC
Published
2025-06-20
Volume
21
Issue
12
Pages
1948-1956
ISSN
  • 1552-4450
  • 1552-4469
DOI
10.1038/s41589-025-01929-w
Cited by
103
References
13
Language
en
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CoChat. (2026). Citation check: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. https://app.cochat.ai/papers/10.1038/s41589-025-01929-w
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Rettie, S. A., Juergens, D., Adebomi, V., Bueso, Y. F., Zhao, Q., Leveille, A. N., Liu, A., Bera, A. K., Wilms, J. A., Üffing, A., Kang, A., Brackenbrough, E., Lamb, M., Gerben, S. R., Murray, A., Levine, P. M., Schneider, M., Vasireddy, V., Ovchinnikov, S., . . . Bhardwaj, G. (2025). Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. Nature Chemical Biology. https://doi.org/10.1038/s41589-025-01929-w

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