7R9V

Structure of PIK3CA with covalent inhibitor 19

7R9V の概要

• エントリーDOI: 10.2210/pdb7r9v/pdb
• 分子名称: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform, N-[2-(4-{4-[2-amino-4-(difluoromethyl)pyrimidin-5-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}piperazin-1-yl)-2-oxoethyl]-1-(prop-2-enoyl)piperidine-4-carboxamide (2 entities in total)
• 機能のキーワード: pi3k, p110, pik3ca, pip3, transferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 110815.03

構造登録者

Burke, J.E.,McPhail, J.A. (登録日: 2021-06-29, 公開日: 2022-04-06, 最終更新日: 2024-10-09)

主引用文献

Borsari, C.,Keles, E.,McPhail, J.A.,Schaefer, A.,Sriramaratnam, R.,Goch, W.,Schaefer, T.,De Pascale, M.,Bal, W.,Gstaiger, M.,Burke, J.E.,Wymann, M.P.
Covalent Proximity Scanning of a Distal Cysteine to Target PI3K alpha.
J.Am.Chem.Soc., 144:6326-6342, 2022

PubMed Abstract: 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 Å from an ATP-site-directed core module and produce potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors. First, reactive warheads are used to reach out to Cys862 on PI3Kα, and second, enones are replaced with druglike warheads while linkers are optimized. The systematic investigation of intrinsic warhead reactivity (), rate of covalent bond formation and proximity ( and reaction space volume ), 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 , , , and , 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 and outperformed the rapidly metabolized CNX-1351, the only known PI3Kα irreversible inhibitor. Washout experiments in cancer cell lines with mutated, constitutively activated PI3Kα showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds and revealed PI3Kβ-dependent signaling, which was sensitive to TGX221. Compounds and thus qualify as specific chemical probes to explore PI3Kα-selective signaling branches. The proposed approach is generally suited to develop covalent tools targeting distal, unexplored Cys residues in biologically active enzymes.

PubMed: 35353516
DOI: 10.1021/jacs.1c13568

実験手法

X-RAY DIFFRACTION (2.69 Å)