Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here we develop PROTAC degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization towards ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced antiproliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets and pave the way towards new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.

A new class of HCV NS3/4a protease inhibitors containing a P2 to P4 macrocyclic constraint was designed using a molecular modeling-derived strategy. Building on the profile of previous clinical compounds and exploring the P2 and linker regions of the series allowed for optimization of broad genotype and mutant enzyme potency, cellular activity, and rat liver exposure following oral dosing. These studies led to the identification of clinical candidate 15 (MK-5172), which is active against genotype 1−3 NS3/4a and clinically relevant mutant enzymes and has good plasma exposure and excellent liver exposure in multiple species.KEYWORDS: hepatitis C, HCV, MK-5172, macrocycle, genotype 3a, mutant enzymes H epatitis C virus (HCV) is a chronic liver infection that affects an estimated 130−170 million people worldwide. 1,2 HCV displays a high degree of genetic heterogeneity and can be classified into six major genotypes with different geographic distributions: genotypes 1, 2, and 3 account for more than 90% of the infections in the developed world. Treatment for HCV is based on combination therapy with pegylated interferon-α and ribavirin. 3 Sustained viral response is seen in ∼45% of HCV genotype 1-infected patients treated for 48 weeks and in ∼80% of genotype 2-and 3-infected patients treated for 24 weeks. Interferon and ribavirin therapy is also associated with a number of serious side effects, limiting the number of patients who may be treated. 4 There is a compelling medical need for new oral therapeutic agents with improved efficacy and tolerability. Several promising antiviral targets for HCV have emerged, 5 with NS3/4a protease inhibitors showing perhaps the most dramatic antiviral effects. 6 Clinical proof of concept for this mechanism was first achieved with BILN-2061. 7 Other compounds have entered clinical trials, including telaprevir 8 and boceprevir, 9 both of which are now marketed treatments for use in combination with a standard of care. Compounds currently in development include TMC-435 10 and We have disclosed a molecular modeling-derived strategy that led us to design HCV NS3/4a protease inhibitors that contain the P2 to P4 macrocyclic constraint. 12 This design arose from an analysis of the crystal structure of full-length NS3/4A with and without inhibitors docked in the active site. 13 Our strategy coupled with a modular synthetic approach, which relies on a key ring-closing metathesis (RCM) reaction, 14 allowed for the rapid exploration of these molecules and the identification of clinical candidates, vaniprevir (1) 15,16 and MK-1220 (2). 17 Herein, we describe the discovery of a clinical candidate with broad activity across genotypes (gt) and resistant HCV variants. 18,19 With the development of vaniprevir progressing, we set a goal for the ongoing discovery program to be the identification of a second generation NS3/4a protease inhibitor. We wanted to maintain or improve the PK profile seen with our previous compounds and make significant improvements in activity against the gt 3a enz...

Bivalent PROTACs work drive protein degradation by simultaneously binding a target protein and an E3 ligase and forming a productive ternary complex. We hypothesized that increasing binding valency within a PROTAC could enhanced degradation. Here, we designed trivalent PROTACs consisting of a bivalent BET inhibitor and an E3 ligand, tethered via a branched linker. We identified VHL-based SIM1 as a low picomolar BET degrader, with preference for BRD2. Compared to bivalent PROTACs, SIM1 showed more sustained and higher degradation efficacy, which led to more potent anti-cancer activity. Mechanistically, SIM1 simultaneously engages with high avidity both BET bromodomains in a cis intramolecular fashion and forms a 1:1:1 ternary complex with VHL exhibiting positive cooperativity and high cellular stability with prolonged residence time. Collectively, our data along with favorable in vivo pharmacokinetics demonstrate that augmenting the binding valency of proximity-induced modalities can be an enabling strategy for advancing functional outcomes.

A new class of HCV NS3/4a protease inhibitors which contain a P2 to P4 macrocyclic constraint was designed using a molecular-modeling derived strategy. Exploration of the P2 heterocyclic region, the P2 to P4 linker, and the P1 side chain of this class of compounds via a modular synthetic strategy allowed for the optimization of enzyme potency, cellular activity, and rat liver exposure following oral dosing. These studies led to the identification of clinical candidate 35b (vaniprevir, MK-7009), which is active against both the genotype 1 and genotype 2 NS3/4a protease enzymes and has good plasma exposure and excellent liver exposure in multiple species.