Abstract 4504: The impact of metabolite kinetics on dysregulation of essential enzymes in cancers with MTAP deficiencies

Background: Methylthioadenosine phosphorylase (MTAP) deletion is a common genetic alteration in various cancers, leading to accumulation of methylthioadenosine (MTA) and dysregulation of protein arginine methyltransferase 5 (PRMT5), an essential enzyme that utilizes the MAT2A product S-adenosylmethionine (SAM). This study investigates the complex interplay between metabolite kinetics and enzyme inhibition in MTAP-deficient cancers, focusing on the efficacy of MTA-cooperative PRMT5 inhibitors and their combination with the MAT2A inhibitor IDE397. Methods: We employed a multi-faceted approach including molecular mutagenesis, surface plasmon resonance (SPR), X-ray crystallography, molecular dynamics simulations, NanoBRET assays, and cell-based studies to elucidate the mechanisms of metabolite exchange and inhibitor binding in PRMT5. The effects of MTA/SAM ratios on PRMT5 inhibitor efficacy were examined, and combination studies with IDE397, an allosteric MAT2A inhibitor, were conducted. Results: Our findings revealed that metabolite exchange in PRMT5 is possible even in the presence of MTA-cooperative inhibitors. Crystallographic and molecular dynamics studies identified a second access channel to the metabolite binding pocket, gated by Lysine 393, allowing for metabolite exchange in the presence of substrate-binding inhibitors. The efficacy of MTA-cooperative PRMT5 inhibitors in cell-based assays was significantly influenced by the ratio of MTA to SAM, not just by absolute MTA concentration. Co-treatment with IDE397 lowered SAM levels in cells, substantially enhancing the efficacy of MTA-cooperative PRMT5 inhibitors. Conclusions: This study provides novel insights into the metabolic vulnerabilities of MTAP-deficient cancers and the mechanisms underlying the efficacy of targeted therapies. The discovery of the metabolite exchange channel in PRMT5 and the impact of MTA/SAM ratios on inhibitor efficacy offer new avenues for drug design and combination strategies. The synergistic effect observed with concurrent MAT2A and PRMT5 inhibition presents a promising approach with the potential to profoundly alter the treatment landscape for patients with MTAP deleted cancers. Our novel findings in this study provide mechanistic support for the importance of understanding metabolite exchange in PRMT5, the crucial impact of MTA/SAM ratios on the potency of MTA-cooperative PRMT5 inhibitors, and the benefit of combination therapy with the MAT2A inhibitor IDE397. Citation Format: Oscar Aubi, Shannon Faris, Daniel M. Walden, Kai Yang, Zhipeng Fang, Mason J. Appel, Angelica M. Gonzalez-Sanchez, Kelly S. Trego, Briana E. Marinoni, Brittany Cruzan, Pari Lanham, Khristina Magallanes, Damien Garbett, Ivan G. Shabalin, Rebeca M. Choy, Peter Teriete. The impact of metabolite kinetics on dysregulation of essential enzymes in cancers with MTAP deficiencies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4504.