Targeted protein degradation via intramolecular bivalent glues

Targeted protein degradation is a pharmacological modality based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via bifunctional compounds (PROTACs) composed of two separate warheads that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target[1][1]–[4][2]. Using orthogonal genetic screening, biophysical characterization, and structural reconstitution, we investigate the mode of action of bifunctional BRD2/4 degraders (IBG1-4) and find that – instead of connecting target and ligase in trans as PROTACs do – they simultaneously engage two adjacent domains of the target protein in cis . This conformational change glues BRD4 to the E3 ligases DCAF11 or DCAF16, leveraging intrinsic target-ligase affinities which, albeit pre-existing, do not translate to BRD4 degradation in absence of compound. Structural insights into the ternary BRD4:IBG1:DCAF16 complex guided the rational design of improved degraders of low picomolar potency. We thus introduce a new modality in targeted protein degradation, termed intramolecular bivalent glues (IBGs), which work by bridging protein domains to enhance surface complementarity with E3 ligases for productive ubiquitination and degradation. ### Competing Interest Statement A.C. is a scientific founder, shareholder and advisor of Amphista Therapeutics, a company that is developing targeted protein degradation therapeutic platforms. The Ciulli laboratory receives or has received sponsored research support from Almirall, Amgen, Amphista Therapeutics, Boehringer Ingelheim, Eisai, Merck KaaG, Nurix Therapeutics, Ono Pharmaceutical and Tocris-Biotechne. A.T. is currently an employee of Amphista Therapeutics. G.E.W. is scientific founder and shareholder of Proxygen and Solgate. The Winter lab received research funding from Pfizer. Source data for [Fig. 1c][3], [Fig. 2b, c][4], [Fig. 5d][5], [Extended Data Fig. 2a][6] and [Extended Data Fig. 6f][7] are included in the Supplementary information files of the manuscript. Cryo-EM density maps are deposited in the EMDB with the accession code EMD-17172 and will be released upon publication. The atomic model is deposited under Protein Data Bank ID 8OV6. Raw micrographs and particle stacks will be available in the EMPIAR-database. Quantitative proteomics data have been deposited to the ProteomeXchange Consortium PRIDE repository[50][8] with the accession ID PXD040570. [1]: #ref-1 [2]: #ref-4 [3]: #F1 [4]: #F2 [5]: #F5 [6]: #F7 [7]: #F11 [8]: #ref-50