Structure-Guided Design of Highly Selective and Potent Covalent Inhibitors of ERK1/2

Abstract

The RAS/RAF/MEK/ERK signaling pathway has been targeted with a number of small molecule inhibitors in oncology clinical development across multiple disease indications. Importantly, cell lines with acquired resistance to B-RAF and MEK inhibitors have been shown to maintain sensitivity to ERK1/2 inhibition by small molecule inhibitors. There are a number of selective, noncovalent ERK1/2 inhibitors reported along with the promiscuous hypothemycin (and related analogues) that act via a covalent mechanism of action. This article reports the identification of multiple series of highly selective covalent ERK1/2 inhibitors informed by structure-based drug design (SBDD). As a starting point for these covalent inhibitors, reported ERK1/2 inhibitors and a chemical series identified via high-throughput screening were exploited. These approaches resulted in the identification of selective covalent tool compounds for potential in vitro and in vivo studies to assess the risks and or benefits of targeting this pathway through such a mechanism of action.

Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors

“…Greater potency on cells than on isolated enzyme is suggestive of substantial off-target activity. Compared to our inhibitors, 5Z7 strongly inhibited the growth of the KRAS G12D Ba/F3 cells without obvious IL-3 rescue suggesting little targeted specificity, while the reported MEK1/2 inhibitor AZD6244 (AZD) [16] or the ERK1/2 inhibitor BVD523 (BVD) [17] exhibited good or moderate potency respectively (Table 1). These results demonstrate that this series of inhibitors is capable of potently inhibiting the proliferation of KRAS G12D Ba/F3 cells but that inhibition of TAK1 is not the sole determinant of this activity.…”

Tetrahydropyrrolo-diazepenones as inhibitors of ERK2 kinase

“…Other preclinical inhibitors have also been reported, 8 including a covalent inhibitor. 9 We recently reported on the structural evolution of a highly compact tetrahydropyrazolopyridine based ERK2 inhibitor. 10 As part of an ERK2 kinase inhibitor program, we identified tetrahydropyrrolo-diazepenones (THPD's) as a promising scaffold.…”

A high throughput assay to identify substrate-selective inhibitors of the ERK protein kinases

“…These compounds include ulixertinib (BVD-523, an analog of the earlier generation compound VTX-11e) and ravoxertinib (GDC-0994) currently in early clinical trials [13, 38] as well as other preclinical compounds [39–44]. Another ATP-competitive inhibitor, SCH772984, was discovered through elaboration of a hit compound identified to bind to the unphosphorylated inactive form of ERK2 using a novel mass spectrometry-based approach [12, 45–47].…”