Abstract 2943: Interrogative Biology® platform identifies a novel target in the ubiquitin pathway and its utility in cancer is supported by small molecule modulators
Authors: Gesta Stephane , Sharma Shefali , Sundararajan Pragalath , Huang Mingshu , Gray Kayleigh , Nastke Maria , Guven Arcan , Diers Anne , Kazerounian Shiva , Hazarika Suwagmani , Grund Eric M. , Vishnudas Vivek K. , Narain Niven R. , Sarangarajan Rangaprasad 
Published: September 2020

Identification of novel therapeutic targets for the development of drugs with a large spectrum of applications in oncology is extremely difficult due, in part, to the complex and heterogenous etiology of the disease. To address this, we interrogated in vitro cancer models representative of multiple tumor types (HepG2, MIA PaCa2, SKMEL28, SCC-25, SkBr-3 MCF7, PC-3, and LnCAP) and compared them to non-tumorigenic and primary cells. Proteomic profiling of these models under various cancer relevant perturbations and analysis through a Bayesian Artificial Intelligence algorithm (Interrogative Biology® platform) allowed the generation of causal inference networks which identified BPM42522 as potential therapeutic target. The anticancer potential of BPM42522, an enzyme in the ubiquitin proteasomal system, was then validated through molecular and pharmacological modulation. siRNA mediated knockdown of BPM42522 resulted in a 50% decrease in cell number in MIA PaCa2 cells and a 30% decrease in cell number in SKHEP1 and HepG2 cells at 96h post transfection. This effect was the result of a robust G2/M cell cycle arrest associated with increased CyclinB1 expression. In addition, a modest increased in apoptosis/necrosis (6-8%) was observed in cells with BPM42522 knockdown. Using Fragment-Based Ligand Discovery, we developed a series of compounds modulating BPM42522 activity and exhibiting anti-cancer properties. A panel of cells lines (Oncolines™) was used to evaluate the potency of our optimized lead compounds. Of 102 cell lines, treatment with optimized lead molecules for 72h reduced the viability of 76 cells lines by more than 70% with an IC50 ranging from 17nM to 318nM. Additional studies on a selected panel of cancer cell lines, upon treatment with modulators, demonstrated that this effect was the result of a G2/M arrest occurring as early as 5h and significantly different by 24h. The accumulation of cells in G2/M was confirmed by increased expression of CyclinB1 and phospho-histone H3 in a dose dependent manner. Furthermore, this increase in G2/M arrest was followed by an increase in apoptosis which could be observed within 24h and progressed until 72h. Identification of BPM42522 as a target for cancer and development of small molecule modulators demonstrates the utility of BERG's Interrogative Biology® platform in elucidating fundamental biology to identify novel therapeutic targets, based on causality, with broad anti-cancer properties.

Citation Format: Stephane Gesta, Shefali Sharma, Pragalath Sundararajan, Mingshu Huang, Kayleigh Gray, Maria Nastke, Arcan Guven, Anne Diers, Shiva Kazerounian, Suwagmani Hazarika, Eric M. Grund, Vivek K. Vishnudas, Niven R. Narain, Rangaprasad Sarangarajan. Interrogative Biology® platform identifies a novel target in the ubiquitin pathway and its utility in cancer is supported by small molecule modulators [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2943.