Potent and Selective Covalent Quinazoline Inhibitors of KRAS G12C

Abstract

Targeted covalent small molecules have shown promise for cancers driven by KRAS G12C. Allosteric compounds that access an inducible pocket formed by movement of a dynamic structural element in KRAS, switch II, have been reported, but these compounds require further optimization to enable their advancement into clinical development. We demonstrate that covalent quinazoline-based switch II pocket (SIIP) compounds effectively suppress GTP loading of KRAS G12C, MAPK phosphorylation, and the growth of cancer cells harboring G12C. Notably we find that adding an amide substituent to the quinazoline scaffold allows additional interactions with KRAS G12C, and remarkably increases the labeling efficiency, potency, and selectivity of KRAS G12C inhibitors. Structural studies using X-ray crystallography reveal a new conformation of SIIP and key interactions made by substituents located at the quinazoline 2-, 4-, and 7-positions. Optimized lead compounds in the quinazoline series selectively inhibit KRAS G12C-dependent signaling and cancer cell growth at sub-micromolar concentrations.

Defining and targeting adaptations to oncogenic KRASG12Cinhibition using quantitative temporal proteomics

“…To confirm efficient block of KRAS activity, we assessed MAPK and PI3K pathways by western blot ( Figure 1D). KRASi induced an upward electrophoretic shift in the KRAS band as a consequence of covalent binding of the inhibitor to KRAS (Zeng et al, 2017), confirming target engagement. ERK1/2 phosphorylation (Thr202/Tyr204) was decreased, consistent with downregulation of the MAPK pathway ( Figure 1D).…”

Targeted Therapies for Pancreatic Cancer and Hurdles Ahead

“…Allosteric compounds that access an inducible pocket formed in the structureof KRAS, have been reported, but these compounds require further optimization to enable their advancement into drugs that can be used in the clinic. Recently, covalent inhibitors of KRAS G12C have been reported (47,48) a few of which could be tested in clinical trials by 2020.…”

An activity-guided map of electrophile-cysteine interactions in primary human immune cells

“…We recently described an efficient strategy to globally assess the ligandability of cysteines in native biological systems that leverages broadly reactive, electrophilic small-molecule fragments referred to as "scouts" Bar-Peled et al, 2017). Two scout fragments bearing an a-chloroacetamide (KB02) or acrylamide (KB05) (Figure 2A, 2B) -reactive groups frequently found in covalent chemical probes and drugs (Baillie, 2016;Chen et al, 2017;Honigberg et al, 2010;Ostrem et al, 2013;Xu et al, 2019;Yang et al, 2014;Zeng et al, 2017) -were used to construct in-depth cysteine ligandability maps across primary human T cells in both control and activated states. We analyzed scout fragment-cysteine interactions using two complementary chemical proteomic methods that provided a balance of confidence in quantitative accuracy (isoTOP-ABPP) with greater multiplexing capacity (TMT-ABPP) (Figures 2A and S2A, B).…”