Recently the ZoBio team made an important contribution to a drug discovery project for our client Mirati Therapeutics that we are particularly proud of and has had significant impact [1]. This work describes a program to develop inhibitors of the epigenetic target PRMT5 with the potential to specifically target cancers with an MTAP gene deletion, providing a precision medicine for these patients with the potential for improved therapeutic index over earlier PRMT5 inhibitors. PRMT5 is an arginine (R) methyl transferase that is a well validated oncology target. A significant portion of human tumours result from deletion of all or parts of the tumour suppressor CDKN2A, which due to its proximity to a gene called MTAP, often results in co-deletion of the latter. MTAP encodes an enzyme that degrades methylthioadenine (MTA), which represents the “business end” of S-adenosyl methionine (SAM), the source of the methyl group for all methyl transferase enzymes. Therefore, in MTAP deleted cells the concentration of MTA, which binds the co-factor site of PRMT5, is greatly increased with respect to healthy cells. The goal of the project was to take advantage of this situation by generating MTA dependent inhibitors of PRMT5.

Mirati’s discovery team utilized a Fragment Based Drug Discovery approach, a technology for which ZoBio’s expertise is widely recognized. In this project we supported Mirati’s internal efforts with additional protein production, hit generation via an SPR screen of our fragment library, X-ray crystallography for SBDD and perhaps most innovatively, a biophysical assay to shed light on the mechanism of MTA dependence of the clinical candidate developed by the client. The compound, MRTX1719, exhibited a roughly 70x preferential killing of MTAP deleted cells over genetically identical cells harbouring a WT MTAP gene. The ZoBio assay team of Masa Kobayashi and Ronald Jean Baptiste were tasked with determining the on and off rates for this compound with sub pM affinity binding to MTA or SAM-bound PRMT5. Given the residence time of many days of the drug on the enzyme complex, a standard SPR assay would not work. Instead, the team implemented a so-called “chaser” assay, in which a compound with a fast off-rate is used to probe the amount of binding site available at various points over time. Such an assay can be referenced to an apo protein, thereby cancelling out both instrumental drift and stochastic functional degradation of the enzyme population. Using this assay, we could determine accurate affinities and (off-rates) of MRTX1719 of 0.14 pM (14 days) and 9.4 pM (4.6 days) for MTA and SAM bound PRMT5 respectively. The ratio of affinities is 67x, thereby neatly explaining the selectivity for MTAP deleted cell killing.

This exciting new compound has begun clinical trials this year and has the potential to bring hope to patients with MTAP-deleted cancers.

[1] – Smith et al., “Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP-Deleted Cancers”, J. Med. Chem., 65, p. 1749, 2022