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Publication Abstract from PubMed

Covalent protein kinase inhibitors exploit currently noncatalytic cysteines in the adenosine 5'-triphosphate (ATP)-binding site via electrophiles directly appended to a reversible-inhibitor scaffold. Here, we delineate a path to target solvent-exposed cysteines at a distance >10 A from an ATP-site-directed core module and produce potent covalent phosphoinositide 3-kinase alpha (PI3Kalpha) inhibitors. First, reactive warheads are used to reach out to Cys862 on PI3Kalpha, and second, enones are replaced with druglike warheads while linkers are optimized. The systematic investigation of intrinsic warhead reactivity (kchem), rate of covalent bond formation and proximity (kinact and reaction space volume Vr), and integration of structure data, kinetic and structural modeling, led to the guided identification of high-quality, covalent chemical probes. A novel stochastic approach provided direct access to the calculation of overall reaction rates as a function of kchem, kinact, Ki, and Vr, which was validated with compounds with varied linker lengths. X-ray crystallography, protein mass spectrometry (MS), and NanoBRET assays confirmed covalent bond formation of the acrylamide warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351, the only known PI3Kalpha irreversible inhibitor. Washout experiments in cancer cell lines with mutated, constitutively activated PI3Kalpha showed a long-lasting inhibition of PI3Kalpha. In SKOV3 cells, compounds 19 and 22 revealed PI3Kbeta-dependent signaling, which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kalpha-selective signaling branches. The proposed approach is generally suited to develop covalent tools targeting distal, unexplored Cys residues in biologically active enzymes.

Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kalpha.,Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP J Am Chem Soc. 2022 Mar 30. doi: 10.1021/jacs.1c13568. PMID:35353516^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.