Reversible Small Molecule pan-Ras Inhibitors Display Tunable Affinity for the Active and Inactive forms of Ras.

14 November 2024, Version 2

Abstract

Activating mutations of Ras are one of the most prevalent drivers of cancer and are often associated with poor clinical outcomes. Despite FDA approval for two irreversible inhibitors that target the inactive state of KRasG12C, significant unmet clinical need still exists, and the susceptibility of non-G12C mutants to inactive-state inhibition remains unclear. Here we report the discovery of a novel series of reversible inhibitors that bind in an enlarged version of the switch I-II pocket with nanomolar affinities. Dependent on chemotype these can either preferentially bind to the inactive or active state or bind both with similar affinity. The active-state binders inhibit the Raf interaction for wild-type Ras, and a broad range of oncogenic KRas mutants with nanomolar potency. A sub-series of these molecules displays cellular inhibition of Ras-Raf binding, as well as decreased phosphorylation of the downstream protein ERK, demonstrating that potent pan-Ras inhibitors can be accessed from this novel pocket.

Keywords

KRAS
Macrocycle
NanoBiT
RAS-ON
Drug discovery
Fragment-Based Drug Discovery
Medicinal Chemistry
Biophysical assays
HSQC Protein-observed NMR
Cancer
Oncogene

Supplementary materials

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Supporting Information
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Supplementary figures, charts, tables, biophysical, bio-logical and biochemical data; Pull-down assay, 3D sphe-roid generation and Cell Titer Glo, in vitro and in vivo as-say information; X-ray data collection and refinement statistics; analytical data for compounds 1, 5; Experimental procedures for compounds 50, 58, 63a, 63b, 83, 87; 1H, 13C NMR spectra and HPLC traces for compounds 1–36 (PDF) Accession codes KRas ligand complex crystal structures have been depos-ited in the wwPDB with the following identifiers: 9GGT (8), 9GGU (9), 9G0Y (11), 9GGV (14), 9G4B (15), 9GGW (16), 9GGX (19), 9GGY (29), 9GGZ (31), 9GH0 (32), 9GH1 (34), 9GH2 (36).
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