Abstract A170: Discovery of small molecule inhibitors of ADAR1
Authors: Buker Shane M , Blakemore Stephen J , Boriack-Sjodin P. Ann , Collins Cindy , Copeland Robert A , Duncan Kenneth W , Ericsson Anna , Garadino Alexandra , Greene-Colozzi April , Leger Nathalie , Lockbaum Gordon , Raman Anugraha , Ribich Scott , Sickmier Allen , Sparling Brian S , Wu Jie , Silver Serena 
Published: December 2023

Background: Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine in double-stranded (ds) RNA. Cellular dsRNAs are edited by ADAR1 to prevent their recognition by cytoplasmic dsRNA sensors such as MDA5 and PKR. Loss of ADAR1 has been shown to induce the activation of these sensors in cancer cells with high intrinsic type 1 interferon signaling, leading to cell death. Accent has developed a Type I Interferon Stimulated Gene (TISG) score through analysis of publicly available datasets that is predictive of sensitivity to ADAR1 loss. As 15-30% of primary tumors in TCGA display elevated type I interferon signaling, ADAR1 has become an attractive oncology target. Here we describe the development of an in vitro and cellular assay suite that was used to progress chemical matter identified from a high-throughput screen (HTS) into single-digit nanomolar inhibitors of cellular ADAR1.

Materials and Methods: A HAP-1 cell model of ADAR1 loss was used in rescue experiments to validate a small molecule inhibition approach towards the targeting of ADAR1 activity. A high-throughput screening-compatible biochemical assay was developed and applied to screen diversity libraries, leading to the identification of a chemical series of ADAR1 inhibitors. The mechanism of inhibition of the series was characterized by substrate-competition and orthogonal substrate binding assays. Iterative optimization of the series resulted in cell-permeable compounds of sufficient potency to be tested in a suite of ADAR1 cellular assays.

Results: ADAR1 loss or catalytic site-mutant cells were more sensitive to exogenous Interferon-β than parental cells, leading to decreased growth and viability of HAP-1 cells. We demonstrate knock-out of ADAR1 or loss of catalytic activity results in activation of PKR upon interferon-β treatment in the HAP-1 model, unlike parental cells. Development of a label-free biochemical assay of sufficient sensitivity to be run under steady-state conditions, showing linear reaction progress curves over multiple rounds of ADAR1 turnover, enabled high-throughput screening. A hit series was identified that showed RNA substrate non-competitive behavior in orthogonal RNA binding assays. To further assist understanding of series mechanism, a crystallization system was developed that produced a novel human ADAR1 structure to 1.45Å resolution. A suite of in vitro and cellular assays were used to further optimize and identify small molecules with   robust inhibition of cellular ADAR1, as read out by cellular RNA editing assays, as well as activation of downstream dsRNA sensor pathways: secretion of interferon B and phosphorylation of PKR. Consistent with our target hypothesis, treatment of the TISG-high squamous cell carcinoma OE21 cell line with potent ADAR1 inhibitors results in cell growth inhibition.

Conclusions: Accent developed a suite of assays that led to the identification of small molecule inhibitors targeting ADAR1.

Citation Format: Shane M Buker, Stephen J Blakemore, P. Ann Boriack-Sjodin, Cindy Collins, Robert A Copeland, Kenneth W Duncan, Anna Ericsson, Alexandra Garadino, April Greene-Colozzi, Nathalie Leger, Gordon Lockbaum, Anugraha Raman, Scott Ribich, Allen Sickmier, Brian S Sparling, Jie Wu, Serena Silver. Discovery of small molecule inhibitors of ADAR1 [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A170.