Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A

Abstract

PIP4K2A is an insufficiently studied type II lipid kinase that catalyzes the conversion of phosphatidylinositol-5-phosphate (PI5P) into phosphatidylinositol 4,5-bisphosphate (PI4,5P2). The involvement of PIP4K2A/B in cancer has been suggested, particularly in the context of p53 mutant/null tumors. PIP4K2A/B depletion has been shown to induce tumor growth inhibition, possibly due to hyperactivation of AKT and reactive oxygen species-mediated apoptosis. Herein, we report the identification of the novel potent and highly selective inhibitors BAY-091 and BAY-297 of the kinase PIP4K2A by high-throughput screening and subsequent structure-based optimization. Cellular target engagement of BAY-091 and BAY-297 was demonstrated using cellular thermal shift assay technology. However, inhibition of PIP4K2A with BAY-091 or BAY-297 did not translate into the hypothesized mode of action and antiproliferative activity in p53-deficient tumor cells. Therefore, BAY-091 and BAY-297 serve as valuable chemical probes to study PIP4K2A signaling and its involvement in pathophysiological conditions such as cancer.

Beyond PI3Ks: targeting phosphoinositide kinases in disease

“…Glioblastoma (GBM) brain tumours downregulate PI5P4Kα compared with normal tissue, with PI5P4Kα playing a tumour suppressor role 119 . Finally, the potent and selective PI5P4K inhibitors developed by Bayer did not show antiproliferative effects on p53 null tumour cells 107 , suggesting either that the antitumour effect requires complete loss of both PI5P4Kα and PI5P4Kβ as found in the genetic ablation models, or that inhibitors have to potently inhibit both PI5P4Kα and PI5P4Kβ isoforms to have an antitumour effect. Continued development of well-validated isoform-selective inhibitors will be crucial in defining any therapeutic opportunities.…”

“…The PI5P4Ks have become attractive drug targets in p53 null tumours and are implicated as key regulators of metabolism 82,101,102 . Early-phase small-molecule inhibitors are being explored in preclinical studies, including pan-PI5P4K inhibitors 101,[103][104][105] and isoform-specific PI5P4K inhibitors [106][107][108][109][110] (Table 2). The optimization of drug analogues has produced new collections of tool compounds 105,111 ; however, PI5P4K inhibitors have yet to advance to the clinical setting.…”

“…The best and most selective PI5P4K inhibitor available is the 1,7-naphthyridinebased inhibitor BAY-091 (Fig. 3c) developed by Bayer, although its selectivity for PI5P4K isoforms is unknown 107 . PI5P4K isoform-specific inhibitors are also in preclinical development.…”

PI(4,5)P2-dependent and -independent roles of PI4P in the control of hormone secretion by pituitary cells

“…The activity of PIP5K1A is blocked by ISA2011B (5) and PIP5K1C by UNC3230 (6). PI5P also contribute to the formation of PI (4,5) P2 by PI4K2A/B, which are inhibited by Bay-091 and Bay-297 (7). PI(4,5)P2 is a substrate for the class I PI3-kinases, consisting of PI3KCA, PI3KCB, PI3KCG, and PI3KCD isoforms.…”

Identification of a chemical probe for lipid kinase phosphatidylinositol-5-phosphate 4-kinase gamma (PI5P4Kγ)

“…While PIP4Kα and PIP4Kβ share 83% identity, PI5P4Kγ only shares 60% identity with either one (Rao et al ., 1998). Examination of the active site residues of the three isoforms revealed minor residue differences in the binding pockets and a more significant difference in the gatekeeper residues (Wortmann et al ., 2021). Pronounced sequence divergence was observed in the P-loop that flanks the ATP site in these kinases (Wortmann et al ., 2021).…”