Journal Article

FZJ-2026-00658

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Accurate de novo design of high-affinity protein-binding macrocycles using deep learning

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.FZJ* ; Willbold, D.FZJ* ; Kritzer, J. A. ; Mougous, J. D. ; Baker, D. (Corresponding author) ; DiMaio, F. (Corresponding author) ; Bhardwaj, G. (Corresponding author)

2025
Nature Publishing Group Basingstoke

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Please use a persistent id in citations: doi:10.1038/s41589-025-01929-w  doi:10.34734/FZJ-2026-00658

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 (Kd < 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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Contributing Institute(s):

1. Strukturbiochemie (IBI-7)

Research Program(s):

1. 5241 - Molecular Information Processing in Cellular Systems (POF4-524) (POF4-524)

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Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DEAL Nature ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 10 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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