Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding

Abstract

Approximately 15% of all human tumors harbor mutant KRAS, a membrane-associated small GTPase and notorious oncogene. Mutations that render KRAS constitutively active will lead to uncontrolled cell growth and cancer. However, despite aggressive efforts in recent years, there are no drugs on the market that directly target KRAS and inhibit its aberrant functions. In the current work, we combined structure-based design with a battery of cell and biophysical assays to discover a novel pyrazolopyrimidine-based allosteric KRAS inhibitor that binds to activated KRAS with sub-micromolar affinity and disrupts effector binding, thereby inhibiting KRAS signaling and cancer cell growth. These results show that pyrazolopyrimidine-based compounds may represent a first-in-class allosteric noncovalent inhibitors of KRAS. Moreover, by studying two of its analogues, we identified key chemical features of the compound that interact with a set of specific residues at the switch regions of KRAS and play critical roles for its high-affinity binding and unique mode of action, thus providing a blueprint for future optimization efforts.

Multi‐target, ensemble‐based virtual screening yields novel allosteric KRAS inhibitors at high success rate

“…One possible mechanism of inhibition by E22 or the rest of the KRAS binders identified in the current work is via effect on GEF‐mediated GDP/GTP exchange, as observed in other indole‐based non‐covalent KRAS binders (Maurer et al., ; Sun et al., ) and andrographolide derivatives. (Hocker et al., ) Another possibility is disruption of effector binding, as shown for a pyrazolopyrimidine‐based compound identified by a similar approach used in this work (McCarthy et al., ). A third possibility, albeit less common, involves inhibition of signaling through the acceleration of the rate of GTP hydrolysis.…”

A potent KRAS macromolecule degrader specifically targeting tumours with mutant KRAS

“…utations of the KRAS oncogene represent more than 85% of all RAS family mutations 1 and individual mutations occur at various codons giving rise to many forms of mutant KRAS protein 2 . Recently, several macromolecules [3][4][5][6][7] and compounds [8][9][10][11][12][13] have been developed that influence the function of RAS family members. Nevertheless, only the G12C mutation of KRAS has been specifically targeted by small molecules by virtue of covalent binding of the compounds to the mutant cysteine [14][15][16][17][18][19][20][21] .…”

Impact of lymphoma‐linked Asn11Tyr point mutation on the interaction between Bcl‐2 and a BH3 mimetic: Insights from molecular dynamics simulation

“…Regions 1, 2, and 3 encircled in red represent the three different levels of orientation change in the ligand induced due to reshaping of the hydrophobic groove in the mutant model [Colour figure can be viewed at wileyonlinelibrary.com] domain and the LA region. Several evidences have been reported where point mutation resulted in significant changes in the conformational changes (Gupta, Prakash, Putkey, & Gorfe, 2019;MaCarthy et al, 2019).…”