A Chemical Probe of CARM1 Alters Epigenetic Plasticity against Breast Cancer Cell Invasion

Abstract

CARM1 is a cancer-relevant protein arginine methyltransferase that regulates many aspects of transcription. Its pharmacological inhibition is a promising anti-cancer strategy. Here SKI-73 is presented as a CARM1 chemical probe with pro-drug properties. SKI-73 can rapidly penetrate cell membranes and then be processed into active inhibitors, which are retained intracellularly with 10fold enrichment for days. These compounds were characterized for their potency, selectivity, modes of action, and on-target engagement. SKI-73 recapitulates the effect of CARM1 knockout against breast cancer cell invasion. Single-cell RNA-seq analysis revealed that the SKI-73-associated reduction of invasiveness act via altering epigenetic plasticity and suppressing the invasion-prone subpopulation. Interestingly, SKI-73 and CARM1 knockout alter the epigenetic plasticity with remarkable difference, arguing distinct modes of action between the small-molecule and genetic perturbation. We therefore discovered a CARM1-addiction mechanism of cancer metastasis and developed a chemical probe to target this process.

Identification of small molecule allosteric modulators of 5,10-methylenetetrahydrofolate reductase (MTHFR) by targeting its unique regulatory domain

“…2 D). (S)-SKI-72 was previously developed as a potent inhibitor of the protein arginine methyltransferase 4 (PRMT4) [ 24 ]. Compared to sinefungin and AdoHcy/AdoMet, ( S )-SKI-72 is further derivatised with an N -benzyl substituent at the 6′ position and substitution at the α-amino carboxylate moiety ( Fig.…”

“…Finally, since ( S )-SKI-72 exhibits poor membrane permeability [ 24 ], we examined the effect of its prodrug derivative (S)-SKI-73, in which the 9′-amine moiety is cloaked with the trimethyl-locked quinone butanoate moiety, on intact HEK293 cells. Previous observations have shown that once (S)-SKI-73 passes inside the cell membrane, it is metabolised into (S)-SKI-72 and 6′-N-benzyl-homosinefungin, which then accumulates inside the cell [ 24 ]. Following 12 or 48 h incubation of (S)-SKI-73 added to the media of HEK293 cells, assay of MTHFR activity from cell lysates revealed no effect on residual MTHFR activity regardless of the concentration of (S)-SKI-73 provided ( Fig.…”

Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

“…Keeping this substitution in designing future nsp14 inhibitors will provide selectivity against PKMTs. WZ16 39 and Compound 8 are PRMT4 (CARM1) inhibitors. Although Compound 8 is a relatively weak nsp14 inhibitor (IC 50 : 95 ± 6 μM) it is likely cell-permeable (US20180305391A1).…”

Rational Design and Synthesis of Selective PRMT4 Inhibitors: a New Chemotype for Development of Cancer Therapeutics

“…The majority of reported PRMT4 inhibitors shows moderate to poor selectivity against other Type I PRMTs 16,17 and/or lack of cellular activity, 18–20 with the notable exceptions of PRMT4 selective chemical probes 1 and 2 reported by Structural Genomics Consortium 14,21 and Epizyme, 15 respectively. Here, we report the development of indole based, potent and PRMT4 selective inhibitors starting from a dual PRMT4/6 inhibitor scaffold.…”