Discovery of a First-in-Class Degrader for the Lipid Kinase PIKfyve

Abstract

The phosphoinositide kinase PIKfyve has emerged as a new potential therapeutic target in various cancers. However, limited clinical progress has been achieved with PIKfyve inhibitors. Here, we report the discovery of a first-in-class PIKfyve degrader 12d (PIK5-12d) by employing the proteolysis-targeting chimera approach. PIK5-12d potently degraded PIKfyve protein with a DC 50 value of 1.48 nM and a D max value of 97.7% in prostate cancer VCaP cells. Mechanistic studies revealed that it selectively induced PIKfyve degradation in a VHL-and proteasome-dependent manner. PIKfyve degradation by PIK5-12d caused massive cytoplasmic vacuolization and blocked autophagic flux in multiple prostate cancer cell lines. Importantly, PIK5-12d was more effective in suppressing the growth of prostate cancer cells than the parent inhibitor and exerted prolonged inhibition of downstream signaling. Further, intraperitoneal administration of PIK5-12d exhibited potent PIKfyve degradation and suppressed tumor proliferation in vivo. Overall, PIK5-12d is a valuable chemical tool for exploring PIKfyve-based targeted therapy.

Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer

“…3C) . Finally, as further confirmation of target specificity, we developed a second-generation proteolysis targeting chimera (PROTAC) degrader of PIKfyve, PIK5-33d, based on our previously described PIKfyve degrader 61 (Extended Data Fig. 3D) .…”

Selective Termination of Autophagy-Dependent Cancers

“…Hence, it can be more effective than chemical inhibitors. This method has been applied to the PIKFYVE protein using the apilimod molecule as bait to deliver the PIKFYVE protein to the E3 ubiquitin ligase [72]. An effective PIKFYVE degrader molecule was developed termed PIK5-12d that strongly bind and degrades PIKFYVE protein (DC50 = 1.5nM) and outperformed both apilimod and YM201636 in suppressing prostate cancer cells growth both in vitro and in vivo.…”

“…Both apilimod and ESK981 have been licensed for clinical applications, thereby demonstrating that temporary inhibition of PIKFYVE is tolerated by humans under conditions in which these drugs exhibit efficacy. Clinical trials for apilimod and ESK981 are in progress for their efficacy against non-Hodgkin lymphoma [6], prostate cancer [9,72], and renal cell carcinoma [110], as well as SARS-CoV-2 [111], and amyotrophic lateral sclerosis [45,112], Therapeutic applications for chemical inhibitors of PIKFYVE, as well as the phosphoinositide 3-kinases (PI3Ks) and phosphoinositide 4-kinases (PI4Ks) (Figure 3C), have been recently reviewed [113]. Data are from the interactive web server 'Gene Expression Profiling Interactive Analysis' [114].…”