In silico design of novel multitarget small molecule inhibitors to treat PTEN-mutant endometrial carcinoma.
Authors: Mujumdar Vaidehi , Delara Ritchie , Dryden Hailey L. , Pal Dhananjaya , Maddeboina Krishnaiah , Arditti Page Mangum , Yada Bharath , Naumann R. Wendel , Casablanca Yovanni , Crane Erin , Brown Jubilee , Durden Donald , McHale Cody 
Published: June 2024

e15119 Background: Previously we described triple CDK4/6-CDK9 inhibitor, LCI133 for the treatment of endometrial carcinoma (EC). We used in silico modeling to optimize LCI133’s physicochemical properties to increase PI3K p110α potency/ADME to better target epithelial-derived cancers, resulting in nanomolar potent LCI139. We characterized LCI139’s in vitro potency, target specificity, activity in in vitro EC models, safety in normal cell lines. Methods: LCI139 + analogs were designed using computational chemistry based on X-ray crystal structures of each target protein + validated chemistry using nuclear magnetic resonance + high-resolution mass spectrometry. Specific target inhibition was assessed by cell-free kinase hotspot/lipid kinase assay + selectivity profile. LCI139 (0.001-10μM) was screened against EC cell lines AN3CA, RL95-2, Ishikawa, KLE, HEC-1-A and -B for 48 hours; IC50 values determined by CellTiter-Glo Assay. EC cells were treated with LCI139 or single agent control for 24 hours + stained with Annexin V/7-AAD to assess apoptosis. Representative PTEN wildtype (HEC-1A) + mutant (AN3CA) EC cell lines were chosen for mechanistic studies + treated 6 to 24 hours with multitarget or single agent inhibitor. Cells were stained with Vybrant DyeCycle Violet to determine cell cycle arrest by cytometer. Cellular lysates were prepared for Western blot (WB). Results: LCI139’s has a molecular weight of 502.57Da + is a highly potent PI3Kα-CDK4/6-CDK9 inhibitor by cell-free kinase assays: 0.070µM (PI3Kα), 0.461µM (PI3Kγ), 0.214µM (PI3Kδ), 0.0015µM (CDK4), 0.0036µM (CDK6), 0.000039µM (CDK9). KINOMEscan revealed a favorable S(35) selectivity score of 0.221 screened against 403 non-mutant kinases. PTEN mutant AN3CA (IC50 216.0nM), RL95-2 (IC50 22.8nM), Ishikawa (IC50 2.5nM) had nanomolar LCI139 IC50 values. PTEN-wild type cell lines were insensitive up to 10μM; confirmed by dose-dependent apoptosis + colony-forming assays. WB revealed LCI139 treatment ablated MCL-1 expression, decreased phosphorylation of AKT, Rb, Rpb1 (Ser2), induced significant amounts of cPARP in PTEN mutant AN3CA. In PTEN-wildtype HEC1A WB, dose-dependent expression of pAKT in PTEN siRNA was noted. LCI139 generated heterogenous cell line specific effects on cell cycle progression + arrest. LCI139 displayed favorable toxicity against normal human kidney cells (HEK-293) compared to single agent controls. Conclusions: Triple PI3K-CDK4/6-CDK9 inhibitor, LCI139, is nanomolar potent against PTEN mutant EC cell lines + displays decreased toxicity compared with CDK9 inhibitor reference compounds, AZD4573 + flavopiridol. Our results merit mechanistic dissection of PTEN interaction with PI3K + CDK9 signaling pathways, cell cycle machinery, CDK9-mediated transcriptional control. These data support extensive in vivo potency, toxicity, PK/PD studies to assess LCI139’s clinical utility in treating EC.