Prmt5-mta Complex

[Kenya Ahyet]

MethylthioadenosinePhosphorylase or MTAP is a gene that frequently suffers homozygous deletion in cancer which results in the accumulation of methylthioadenosine (MTA) within cancer cells. MTA binds to PRMT5 and forms the PRMT5-MTA complex. This new complex creates a novel drug target for the potential treatment of MTAP-deleted cancers.

Cancer cells with MTAP deletion were hypothesized to be sensitive to inhibition of the PRMT5-MTA complex.17,18,19 This is an example of synthetic lethality where the inhibition of two genes results in cell death.

MTAP homozygous deletion occurs in around 10 percent of cancers,20 including a high percentage of non-small cell lung cancer (NSCLC), pancreatic cancer and mesothelioma. MTAP-deleted cancers are associated with a poor prognosis; median survival rates among pan-cancer patients with tumors harboring homozygous co-deletions of 9p21 are significantly lower than the tumors with wildtype 9p21 (24 months vs. 115 months),20 representing a significant unmet medical need.

MRTX1719 is an investigational, internally discovered MTA-cooperative PRMT5 inhibitor that selectively binds the PRMT5-MTA complex, inhibiting PRMT5 function in MTAP-deleted cancer cells. MRTX1719 selectively inhibits the viability of cancer cells with MTAP deletion and is designed to spare healthy, non-tumor cells.21 In pre-clinical studies, MRTX1719 induced tumor regression in cell line and patient-derived xenograft tumor models.22 This differentiated approach may demonstrate a potentially improved therapeutic index in preclinical studies relative to first generation PRMT5 inhibitors.

Here we describe the early stages of a fragment-based lead discovery (FBLD) project for a recently elucidated synthetic lethal target, the PRMT5/MTA complex, for the treatment of MTAP-deleted cancers. Starting with five fragment/PRMT5/MTA X-ray co-crystal structures, we employed a two-phase fragment elaboration process encompassing optimization of fragment hits and subsequent fragment growth to increase potency, assess synthetic tractability, and enable structure-based drug design. Two lead series were identified, one of which led to the discovery of the clinical candidate MRTX1719.

It has been shown that PRMT5 inhibition by small molecules can selectively kill cancer cells with homozygous deletion of the MTAP gene if the inhibitors can leverage the consequence of MTAP deletion, namely, accumulation of the MTAP substrate MTA. Herein, we describe the discovery of TNG908, a potent inhibitor that binds the PRMT5MTA complex, leading to 15-fold-selective killing of MTAP -deleted (MTAP-null) cells compared to MTAP intact (MTAP WT) cells. TNG908 shows selective antitumor activity when dosed orally in mouse xenograft models, and its physicochemical properties are amenable for crossing the blood-brain barrier (BBB), supporting clinical study for the treatment of both CNS and non-CNS tumors with MTAP loss.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

Dr Marx says that MTAP deletion is the most common gene deletion event across several cancer types and is associated with a poor prognosis for patients with this genetic alteration. He explains the rationale of the study; that PRMT5 is an enzyme critical to the survival of both healthy and cancer cells and is partially inhibited by a metabolite called methylthioadenosine (MTA), which specifically accumulates in MTAP-deleted cancers.

Dr Marx then discusses the methodology and results of the study. In the preclinical study, the PRMT5 inhibitor was shown to specifically target and stabilise the PRMT5/MTA complex in MTAP-deleted cancer models.

This is a targeted approach known as synthetic lethality in which a therapeutic agent selectively kills cells with a particular genetic alteration while having minimal to no effect on healthy cells. In the end, Dr Marx mentions that Mirati is advancing its PRMT5 compound toward an IND filing in the first half of 2022.

Last weekend at the virtual AACR meeting we presented our initial preclinical data on our internally discovered potentially first in class approach targeting PRMT5. Our goal, the rationale for this project, is a precision medicine to treat patients with MTAP-deleted cancers. The MTAP deletion is the most common gene deletion across all cancer types and is associated with a very poor prognosis for these patients so new treatments are needed.

First, just a little bit more about PRMT5. PRMT5 is an enzyme that is critical to the survival of both healthy and cancer cells. This enzyme is partially inhibited by a metabolite, methylthioadenosine or MTA, which specifically accumulates only in those cancer cells with an MTAP deletion. So our unique approach, which is represented by the data we showed with MRTX9768 at the AACR meeting, is to specifically and selectively target this PRMT5 MTA complex in those MTAP deleted cancers. So in preclinical studies this molecule demonstrated potent and selective inhibition of cellular growth in vitro and reduction of tumour growth in vivo in those MTAP deleted cancer cells.

This is a preclinical programme and our approach was unprecedented so that required that we develop some basic science and novel project plans to advance it. My colleagues, the great scientists here at Mirati Therapeutics, created, prepared and evaluated several hundreds of new molecules in pursuit of this project over the course of the past several years. The significant medical need is a real motivator for us and our desire is to bring hope to patients with these cancers.

The PARP inhibitors are the classic example of the approach using synthetic lethality. In this case the MTAP deleted cancers can be specifically identified in patients and they will represent their own unique subset of patients. But the scientific concept that supports our approach, the synthetic lethality concept, is exemplified by PARP inhibitors.

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Available structural data are insufficient for understanding interactions between a Class 2 inhibitor and MTA. A crystal structure (PDB: 3UA4) of apo C. elegans PRMT5:MEP50 complex differs significantly from that of the liganded human complex45, whereas the apo human complex has been resistant to crystallization. The first structure of the human complex with a SAM analog A9145C and a histone H4 substrate peptide (PDB: 4GQB) was a milestone and triggered competition in X-ray SBDD39,58. However, all published crystal structures of human PRMT5 were obtained in complex with one or more ligands37 and reveal little on their low synergy with MTA.

Besides the accommodation of most or all atoms of the ligands in their densities, ranking of the ligand-protein interaction energy helps define the most stable poses. a Density in the cryo-EM map for MTA. b Overlay of top three poses from the AUTODOCK analysis with the cryo-EM density for MTA (gray). The top pose is in green. c After refinement, the top pose is almost in exactly the same position and orientation as that from the X-ray structure (cyan). Dashed lines represent the H-bonds in the binding pocket. d Top pose of SAH from AUTODOCK agrees with the model from the crystal structure (cyan). e Top pose of SAM from AUTODOCK overlaps very closely with the one in the crystal structure (cyan). f Top three poses of 11-2F out of AUTODOCK overlap relatively well with the cryo-EM map, which was improved after real-space refinement against the cryo-EM density. g/h After optimization in ISOLDE, the top pose (green in g) of 11-2F changes slightly with the quinoline ring rotated by 180 degrees around a rotatable bond (in yellow). A simplified all-atomistic MD optimization in ISOLDE enhances the agreement of the model (green) with the ligand density (h). The dashed lines in g represent key H-bonds for the ligand binding. i Comparison of top poses of MTA from three different software packages (AUTODOCK, SwissDock, and AutoDock Vina). j Top poses of 11-2F from three packages are nearly identical.

As more positive controls of our protocol, we generated top poses of SAH (Supplementary Fig. 3b and Supplementary Table 2) and SAM (Supplementary Fig. 3c and Supplementary Table 3) in the known X-ray structural models, and found that the top pose for each agrees well with the respective X-ray model, except minor differences in the flexible tail regions (Fig. 3d, e). These comparisons support our general strategy and argue strongly that the predictions from ligand docking and energy minimization in AUTODOCK are relatively accurate for ring-containing compounds and can be further improved when cryo-EM densities of sufficient resolutions are available to constrain them.

The strategies we tested above appear to work well for the redesign of 11-2F based on accurate modeling of the protein-ligand interactions and the computational analysis to select three different ways out of virtual modifications to decrease binding energy. The energy minimization defines the energetically favored pose with the 11-2F quinoline ring being next to the tail of MTA. One of three hits from virtual modification, 11-9F, showed significantly better potency in enzyme inhibition assay and strong MTA-synergy, close to the predicted enhancement based on relative binding energy (Table 2 and Fig. 7e). Because of their preserved head parts (quinazoline), HWIem2104 and HWIem2109 are probably going to follow the prediction and show even higher potency than 11-9F, even though they still need to be synthesized for experimental tests.

3a8082e126