A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo

Abstract

Targeted protein degradation offers an alternative modality to classical inhibition and holds the promise of addressing previously undruggable targets to provide novel therapeutic options for patients. Heterobifunctional molecules co-recruit a target protein and an E3 ligase, resulting in ubiquitylation and proteosome-dependent degradation of the target. In the clinic, the oral route of administration is the option of choice but has only been achieved so far by CRBN- recruiting bifunctional degrader molecules. We aimed to achieve orally bioavailable molecules that selectively degrade the BAF Chromatin Remodelling complex ATPase SMARCA2 over its closely related paralogue SMARCA4, to allow in vivo evaluation of the synthetic lethality concept of SMARCA2 dependency in SMARCA4-deficient cancers. Here we outline structure- and property-guided approaches that led to orally bioavailable VHL-recruiting degraders. Our tool compound, ACBI2, shows selective degradation of SMARCA2 over SMARCA4 in ex vivo human whole blood assays and in vivo efficacy in SMARCA4-deficient cancer models. This study demonstrates the feasibility for broadening the E3 ligase and physicochemical space that can be utilised for achieving oral efficacy with bifunctional molecules.

Advancing Strategies for Proteolysis-Targeting Chimera Design

“…The linker can be attached at several exit vectors for both CRBN and VHL ligands. The binding site has an impact on not only PROTAC selectivity but also DMPK parameters, such as microsomal stability . W. Farnaby et al introduced linkers at different locations of the VHL ligand, thereby forming “phenolic series” and “benzylic series” PROTACs for SMARCA2/4 degradation (Figure ).…”

“…Binding between the warhead and the POI does not have to be strong, but POI ligands with low nanomolar affinity are ideal. Notably, de novo design of novel and potent POI ligands with improved physicochemical properties is more likely to arrive at orally available degraders . Besides, for suitable conjugation and optimized physicochemical properties, the structure of the POI ligand can be slightly modified, for example, by replacing a piperidine with an N,N -diethylamino group, a morpholine with piperazine, , or a quaternion ring with a topine ring and octahydropentalen, or by omitting the noncritical o -fluoro substitution (Figure ).…”

A two-faced selectivity solution to target SMARCA2 for cancer therapy

“…Now, two recent papers from Kofink et al and Cantley et al have prospectively targeted the PROTAC-mediated ternary complex to solve the apparently intractable SMARCA2/4 selectivity problem 12 , 13 .…”

“…Kofink et al build on the identification of ACBI1, with the challenging task of achieving both selective SMARCA2 degradation and oral bioavailability 12 . This started with careful selection of the SMARCA2/4 bromodomain binder to minimise hydrogen bond donors and increase rigidity, which has been shown to improve likelihood of increased oral bioavailability for compounds beyond the rule-of-five 15 .…”

Solubility Enhanced Formulation Approaches to Overcome Oral Delivery Obstacles of PROTACs

“…In contrast, oral bioavailability remains limited for PROTACs derived from other E3 ligase handles, such as von Hippel-Lindau (VHL) binders. For instance, the optimized SMARCA2 degrader ACBI2 was still limited in oral bioavailability and aqueous solubility ( Figure 1 ) [ 4 ]. However, to fully unlock the enormous potential of PROTACs, especially in chronic diseases, peroral applications are the yet unmet goal to increase the compliance of patients [ 5 ].…”