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The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here, we present the discovery and characterization of a pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K's reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders. • Inhibitor THZ-P1-2 shows PI5P4K enzyme inhibition and target engagement in cells • THZ-P1-2 covalently targets unannotated cysteines outside the PI5P4K active site • AML/ALL cell lines are broadly sensitive to THZ-P1-2's covalent effects • PI5P4K inhibition causes autophagy disruption and upregulates TFEB signaling PI5P4K, an understudied kinase family, is essential in various disease contexts. Sivakumaren et al. develop and characterize PI5P4K inhibitor THZ-P1-2, which targets unique cysteines, exhibits effects in biochemical and cellular assays, displays anticancer activity in leukemia cell lines, and causes defects in autophagy similar to PI5P4K gene knockdown or deletion. [ABSTRACT FROM AUTHOR]

Insulin stimulates the conversion of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P 2 ) to phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P 3 ), which mediates downstream cellular responses. PI(4,5)P 2 is produced by phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and by phosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). Here, we show that the loss of PIP4Ks (PIP4K2A, PIP4K2B, and PIP4K2C) in vitro results in a paradoxical increase in PI(4,5)P 2 and a concomitant increase in insulin-stimulated production of PI(3,4,5)P 3 . The reintroduction of either wild-type or kinase-dead mutants of the PIP4Ks restored cellular PI(4,5)P 2 levels and insulin stimulation of the PI3K pathway, suggesting a catalytic-independent role of PIP4Ks in regulating PI(4,5)P 2 levels. These effects are explained by an increase in PIP5K activity upon the deletion of PIP4Ks, which normally suppresses PIP5K activity through a direct binding interaction mediated by the N-terminal motif VMLΦPDD of PIP4K. Our work uncovers an allosteric function of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P 2 synthesis and insulin-dependent conversion to PI(3,4,5)P 3 and suggests that the pharmacological depletion of PIP4K enzymes could represent a strategy for enhancing insulin signaling., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)