Discovery and Characterisation of Highly Cooperative FAK‐Degrading PROTACs

Abstract

Focal adhesion kinase (FAK) is a key mediator of tumour progression and metastasis. To date, clinical trials of FAK inhibitors have reported disappointing efficacy for oncology indications. We report the design and characterisation of GSK215, a potent, selective, FAK‐degrading Proteolysis Targeting Chimera (PROTAC) based on a binder for the VHL E3 ligase and the known FAK inhibitor VS‐4718. X‐ray crystallography revealed the molecular basis of the highly cooperative FAK‐GSK215‐VHL ternary complex, and GSK215 showed differentiated in‐vitro pharmacology compared to VS‐4718. In mice, a single dose of GSK215 induced rapid and prolonged FAK degradation, giving a long‐lasting effect on FAK levels (≈96 h) and a marked PK/PD disconnect. This tool PROTAC molecule is expected to be useful for the study of FAK‐degradation biology in vivo, and our results indicate that FAK degradation may be a differentiated clinical strategy versus FAK inhibition for the treatment of cancer.

Advancing Strategies for Proteolysis-Targeting Chimera Design

“…24 Rigid linkers can lead to more effective degradation, as seen for compounds 46 (GSK215, Figure 9) and 47 (DGY-09-192, Figure 9). 68,69 Furthermore, nitrogen heterocycles are beneficial for increasing solubility and improving oral bioavailability. Wang et al reported two orally bioavailable AR degraders, compounds 48 (ARD-2128, Figure 10) and 49 (ARD-2585, Figure 10).…”

“…Compound 46 (see Figure 12) is a potent FAK degrader (DC 50 = 1.3 nM, DC max = 99%) and induced high ternary complex cooperativity as a result of various de novo protein−protein interactions in the cocrystal, including van der Waals interactions, direct H bonds, and salt bridges. 68 These suggest that de novo protein−protein interactions and "cross" protein− ligand interactions are crucial for more potent degrader discovery and should be considered seriously in PROTAC design.…”

PROTAC’ing oncoproteins: targeted protein degradation for cancer therapy

“…In 2021, Law et al discovered the VHL-dependent FAK degrader GSK215 ( 56 ) by derivatizing a previously reported 2,4-diaminopyridine FAK inhibitor [ 211 , 212 ]. Therein, alkyl and PEG-based linkers ranging in length between two and fourteen atoms were explored.…”

Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

“…Thirteen PROTAC ternary complex crystal structures were extracted from the PDB 27 , selected based on three criteria: (1) that the crystal structure contained an E3 ligase, a ligand molecule, and a target; (2) that the crystal structure resolution was below 4 Å and (3) that the ligand was a PROTAC and not a molecular glue. The dataset is composed of three types of E3 ligases (9 VHL 17,[54][55][56][57][58][59] , 2 Cereblon 60-63 and 2 cIAP 64 ), multiple different PROTAC molecules and a diverse set of protein targets, from kinases to bromodomains or proteins implicated in DNA repair (as WRD5). For the realistic docking case scenario, unbound monomers were selected to be different from the initial 13 crystal structures in terms of interface side-chain packing 54,[64][65][66][67][68][69][70][71] .…”