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001051977 1001_ $$00000-0001-9797-6939$$aRettie, Stephen A.$$b0
001051977 245__ $$aAccurate de novo design of high-affinity protein-binding macrocycles using deep learning
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001051977 520__ $$aDeveloping macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic binders against protein targets of interest. We tested 20 or fewer designed macrocycles against each of four diverse proteins and obtained binders with medium to high affinity against all targets. For one of the targets, Rhombotarget A (RbtA), we designed a high-affinity binder (Kd < 10 nM) despite starting from the predicted target structure. X-ray structures for macrocycle-bound myeloid cell leukemia 1, γ-aminobutyric acid type A receptor-associated protein and RbtA complexes match closely with the computational models, with a Cα root-mean-square deviation < 1.5 Å to the design models. RFpeptides provides a framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.
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001051977 7001_ $$00000-0001-6425-8391$$aJuergens, David$$b1
001051977 7001_ $$0P:(DE-HGF)0$$aAdebomi, Victor$$b2
001051977 7001_ $$00000-0002-2118-2195$$aBueso, Yensi Flores$$b3
001051977 7001_ $$0P:(DE-HGF)0$$aZhao, Qinqin$$b4
001051977 7001_ $$0P:(DE-HGF)0$$aLeveille, Alexandria N.$$b5
001051977 7001_ $$00000-0002-8795-9614$$aLiu, Andi$$b6
001051977 7001_ $$00000-0001-9473-2912$$aBera, Asim K.$$b7
001051977 7001_ $$aWilms, Joana A.$$b8
001051977 7001_ $$0P:(DE-Juel1)181095$$aÜffing, Alina$$b9
001051977 7001_ $$00000-0001-5487-0499$$aKang, Alex$$b10
001051977 7001_ $$0P:(DE-HGF)0$$aBrackenbrough, Evans$$b11
001051977 7001_ $$0P:(DE-HGF)0$$aLamb, Mila$$b12
001051977 7001_ $$00000-0003-0313-6248$$aGerben, Stacey R.$$b13
001051977 7001_ $$00000-0003-1560-6673$$aMurray, Analisa$$b14
001051977 7001_ $$00000-0003-4874-5557$$aLevine, Paul M.$$b15
001051977 7001_ $$00009-0006-9798-852X$$aSchneider, Maika$$b16
001051977 7001_ $$0P:(DE-HGF)0$$aVasireddy, Vibha$$b17
001051977 7001_ $$0P:(DE-HGF)0$$aOvchinnikov, Sergey$$b18
001051977 7001_ $$0P:(DE-Juel1)131988$$aWeiergräber, Oliver H.$$b19$$ufzj
001051977 7001_ $$0P:(DE-Juel1)132029$$aWillbold, Dieter$$b20
001051977 7001_ $$00000-0003-2878-6781$$aKritzer, Joshua A.$$b21
001051977 7001_ $$00000-0002-5417-4861$$aMougous, Joseph D.$$b22
001051977 7001_ $$00000-0001-7896-6217$$aBaker, David$$b23$$eCorresponding author
001051977 7001_ $$00000-0002-7524-8938$$aDiMaio, Frank$$b24$$eCorresponding author
001051977 7001_ $$00000-0001-6554-2335$$aBhardwaj, Gaurav$$b25$$eCorresponding author
001051977 773__ $$0PERI:(DE-600)2190276-8$$a10.1038/s41589-025-01929-w$$gVol. 21, no. 12, p. 1948 - 1956$$n12$$p1948 - 1956$$tNature chemical biology$$v21$$x1552-4450$$y2025
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