Rational Chemical Design of Molecular Glue Degraders

Abstract

Targeted protein degradation with molecular glue degraders has arisen as powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify chemical handles that would convert protein-targeting ligands into molecular glue degraders of their targets. Using the CDK4/6 inhibitor Ribociclib as a testbed, we identified a covalent handle that, when appended to the exit vector of Ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Covalent chemoproteomic profiling of this CDK4 degrader revealed covalent interactions with cysteine 32 of the RING family E3 ubiquitin ligase RNF126. Optimization of this covalent scaffold led to an improved CDK4 degrader with a methoxyphenyl fumarate handle that showed improved interactions with RNF126. We then identified the minimum covalent chemical handle required for interaction with RNF126. With this knowledge in hand, we transplanted this covalent fumarate handle onto chemically related and un-related protein-targeting ligands to induce the degradation of several proteins across diverse protein classes, including BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, and SMARCA2. Our study undercovers a potential chemical rational design strategy for converting protein-targeting ligands into covalent molecular glue degraders.

Chemical Specification of E3 Ubiquitin Ligase Engagement by Cysteine-Reactive Chemistry

“…Reactive warhead attachment to well-characterized compounds can activate unexpected protein degradation through defined E3 ubiquitin ligases. There has been much recent interest in such a strategy, 14 but the identities of the targeted E3 ligases have been unclear. We have used a combination of synthetic chemistry and unbiased genetic screens to show conclusively that the selectivity for E3 ligases is surprisingly sensitive to covalent chemistry.…”

“…One recent report has taken explicit advantage of this strategy. 14 While looking for cysteine-reactive derivatives of the bromodomain inhibitor JQ1 that induce degradation of the cellular partner of JQ1, BRD4 (Bromodomain-containing protein 4), we found that minor modifications to the appended chemical warhead can direct BRD4 degradation by distinct cellular pathways. While most tested warheads engage DCAF16, we report that cyanoacrylamide warheads enable DCAF11-dependent degradation.…”

Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders

“…Covalency has the potential not only to aid the discovery of molecular glues, but also to impart improved efficacy through strengthening of the interface 17 . Chemo-proteomic studies have indeed identified putative covalent molecular glues 18,19 , but it remains to be shown mechanistically whether these molecules truly act as molecular glues and whether general principles can be derived to aid future discovery.…”

Toward In Silico Design of Protein–Protein Interaction Stabilizers

“…However, there are still urgent needs in computational modeling-assisted MG development. In the accompanying articles of this paper, there are two reports 7,8 that develop MGs based on experimental screening and design. Recently, Wang and co-workers presented PPI-Miner to search potential protein interacting partners utilizing protein structure motif and sequence motif matching.…”