Rational Chemical Design of Molecular Glue Degraders

Abstract

Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasomemediated 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 a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Further modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene-1,4-dione ("fumarate") handle that showed improved interactions with RNF126. Subsequent chemoproteomic profiling revealed interactions of the CDK4 degrader and the optimized fumarate handle with RNF126 as well as additional RING-family E3 ligases. We then transplanted this covalent handle onto a diverse set of protein-targeting ligands to induce the degradation of BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, HDAC1/3, and SMARCA2/4. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.

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

“…Examples of this approach include large-scale chemical biology programs and close investigation of unexplained target degradation in the patent literature. ,, These studies point to an emerging strategy for molecular glue development that depends on the chemical elaboration of an established ligand for a degradation target. One recent report has taken explicit advantage of this strategy …”

PROTAC chemical probes for histone deacetylase enzymes

“…[37][38][39] To date, the majority of protein degradation strategies targeting HDACs has been focused on the design of PROTACs which will also be the focus of this review, however Toriki et al recently reported molecular glues targeting HDAC1 and HDAC3 for degradation. 40 PROTACs designed to degrade their target protein typically contain three components: a ligand to engage the protein of interest (POI), a ligand to initiate protein degradation (most commonly an E3-ligand), and a linker covalently bonding these Fig. 1 Top: Vorinostat, romidepsin, belinostat and panobinostat are drugs that inhibit the HDAC catalytic active site and are FDA approved.…”

“…37–39 To date, the majority of protein degradation strategies targeting HDACs has been focused on the design of PROTACs which will also be the focus of this review, however Toriki et al recently reported molecular glues targeting HDAC1 and HDAC3 for degradation. 40…”

Tracking the mechanism of covalent molecular glue stabilization using native mass spectrometry

“…Recently, the fusion of covalent and molecular glue drug discovery has yielded a new and promising alternative drug discovery approach. 1,12 Briefly, covalent molecular glues incorporate an electrophile that reacts with a nucleophilic amino acid on one of the protein partners. Covalent molecular glues EN450 (ref.…”