Abstract LB137: Orally available, CDK9 selective, small molecule inhibitors shows promise in n-Myc-driven neuroendocrine prostate cancers (NEPC)
Authors: Medley Kyle , Li Zhaoliang , Vankayalapati Saisha , Paritala Sowmya , Yan Dongqing , Coffman Kimberly , Agarwal Neeraj , Bearss David J. 
Published: June 2022

Introduction/Purpose: Amplification of N-MYC causes its overexpression in Neuroendocrine Prostate Cancer (NEPC) patients is prevalent, and it is a rare lethal subtype of cancer detected in 2% of all Prostate Cancers (PC)and over 10-17% of mCRPC (Metastatic Castration-Resistant PC) patients. N-MYC and activated CDK9 act as oncogenic drivers sufficient to transform human-derived prostate cancer cells to take on NEPC phenotypic changes resulting in a more aggressive disease identified in late-stage human PC patients. Additionally, N-MYC is required for tumor resistance, and its downregulation through CDK9 inhibitors lessens the tumor burden. Our efforts in this study have proven that the targeting of N-NYC as a driver of NEPC with CDK9 inhibitors such as BLX-3030 and its series could be a viable approach for therapeutic intervention of mCRPC and NEPCs.

Experimental Procedures: Utilizing our FIELDS fragment-based design strategies, we have developed and synthesized a series of novel small molecule CDK9 agents that reversibly bind to CDK9, competitively block the ATP site, and elicit pharmacological responses in N-MYC and other prostate cancer cells in vitro. CDK9 cell-free kinase binding, CDKs selectivity, pCDK9 inhibition assays were performed and confirmed its on-target efficacy and potency of lead CDK9 inhibitor BLX-3030.

Results and Summary: In these studies, our lead CDK9 kinase inhibitor BLX-3030 from over 60 plus analogs demonstrated potent activity with an IC50 of &lt;5 nM in inhibiting CDK9. CDK9 and N-MYC expression has been detected in PC-3, DU-145, LNCaP, and in LASCPC-01, NCI-H660 and 22RV1 cell lines. HCI-3030 exhibited potent cellular efficacy with an IC50 of 22 to 590 nM in PC cell lines and in N-MYC expressed cells had an activity of 76, 470, and 132 nM respectively and reduced pCDK9, C-MYC, Mcl-1, N-MYC and its downstream RNA Pol II (Ser-2) and pAR (Ser-81) dose-dependently. Our preliminary results support the hypothesis that inhibition of CDK9 reinstates anti-tumor and blocks tumor progression in both mCRPC and NEPCs cellular models. BLX-3030 and a few of its analogs had excellent PK properties in mouse species in the range of 28-94% F, low clearance, and &gt;3 hours half-life. BLX-3030 is nominated as a pre-clinical agent for additional 3D, FACS/apoptosis, cell migration, live-cell imaging including immunofluorescent studies along with in vivo prostate cancer mouse model efficacy studies as well and these results will be presented.

Conclusions: In summary, a series of BLX-3030, its analogs as CDK9 inhibitors, display a range of potency in prostate cancer and NEPC cells with ideal PK parameters, were identified. Within compounds of this profile, BLX-3030 was selected as a candidate CDK9 inhibitor upon in-depth evaluation of the in vitro and in Vivo PK properties further supporting our conclusion that BLX-3030 had the appropriate qualities for development as a pre-clinical candidate.

Citation Format: Kyle Medley, Zhaoliang Li, Saisha Vankayalapati, Sowmya Paritala, Dongqing Yan, Kimberly Coffman, Neeraj Agarwal, David J. Bearss. Orally available, CDK9 selective, small molecule inhibitors shows promise in n-Myc-driven neuroendocrine prostate cancers (NEPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB137.