Addressing Kinase-Independent Functions of Fak via PROTAC-Mediated Degradation

Abstract

Enzymatic inhibition has proven to be a successful modality for the development of many small-molecule drugs. In recent years, small-molecule-induced protein degradation has emerged as an orthogonal therapeutic strategy that has the potential to expand the druggable target space. Focal adhesion kinase (Fak) is a key player in tumor invasion and metastasis, acting simultaneously as a kinase and a scaffold for several signaling proteins. While previous efforts to modulate Fak activity were limited to kinase inhibitors with low success in clinical studies, protein degradation offers a possibility to simultaneously block Fak’s kinase signaling and scaffolding capabilities. Here, we report the development of a selective and potent Fak degrader, PROTAC-3, which outperforms a clinical candidate, defactinib, with respect to Fak activation as well as Fak-mediated cell migration and invasion. These results underline the potential that PROTACs offer in expanding the druggable space and controlling protein functions that are not easily addressed by traditional small-molecule therapeutics.

Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery

“…Importantly, the PROTAC did not cause degradation of the off‐target binding proteins detected. A similar comparison with a similar conclusion was made for defactinib, a FAK kinase inhibitor, versus a defactinib‐PROTAC analogue …”

“…Importantly,t he PROTAC did not cause degradation of the off-target binding proteins detected.Asimilar comparison with as imilar conclusion was made for defactinib, aF AK kinase inhibitor,v ersusad efactinib-PROTAC analogue. [103] Despite these points, inhibition of enzyme activity is still an efficacious route to drug discovery. It is relatively simple to perform high-throughput screens for inhibitors of activity,a nd putative off-target effects can also often be counterscreened.…”

Discovery of an AKT Degrader with Prolonged Inhibition of Downstream Signaling

“…Moreover, AKT has been reported to have kinase-independent functions (Vivanco et al, 2014) that would reduce efficacy of small molecule inhibitors, and resistance to AKT inhibitors can arise in some contexts due to upregulation of AKT3 (Stottrup et al, 2016). Degraders have been reported to abrogate kinase-independent functions (Cromm et al, 2018) and overcome inhibitor-induced compensatory upregulation of target proteins (Cai et al, 2012;Han et al, 2019). Targeted AKT degradation may be a promising alternative approach for therapeutic intervention in cancers with PI3K/AKT pathway alterations.…”

“…Heterobifunctional degraders, also known as PROTACs (proteolysis targeting chimeras), consist of a moiety that binds to an E3 ubiquitin ligase chemically linked to a second moiety that engages a target protein, thereby recruiting the E3 ligase into close proximity to the target protein to induce its ubiquitination and subsequent proteasomal degradation (Winter et al, 2015). Several advantages of degraders over inhibitors have been reported, which include enhancing the selectivity of multi-targeted inhibitors (CDK9) (Olson et al, 2018), abrogating non-kinase dependent functions (FAK) (Cromm et al, 2018), and overcoming resistance mutations (BTK) (Dobrovolsky et al, 2018). Because the pharmacological effects of degraders depend on the re-synthesis rate of the targeted protein rather than sustained target occupancy, small molecule degraders may also have significantly prolonged effects in comparison to reversible inhibitors.…”

Rationalizing PROTAC-mediated ternary complex formation using Rosetta

“…Over the past decade, PROTACs have been developed to address an ever-expanding collection of target proteins. Owing to the availability of well-validated chemical matter to repurpose as PROTAC warheads, the majority of early reports focused on degraders of hormone receptors [10][11][12][13], BET-family proteins [14][15][16] and kinases [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. More recently, the applicability of PROTACs has been broadened to include multi-functional proteins (e.g., TRIM24 [34], SMARCA2 [35] tau [36,37]), and HaloTag7-fused proteins for chemical genetics [38].…”