Structure–activity study for (bis)ureidopropyl- and (bis)thioureidopropyldiamine LSD1 inhibitors with 3-5-3 and 3-6-3 carbon backbone architectures

Abstract

Methylation at specific histone lysine residues is a critical post-translational modification that alters chromatin architecture, and dysregulated lysine methylation/demethylation is associated with the silencing of tumor suppressor genes. The enzyme lysine-specific demethylase 1 (LSD1) complexed to specific transcription factors catalyzes the oxidative demethylation of mono- and dimethyllysine 4 of histone H3 (H3K4me and H3K4me2 respectively). We have previously reported potent (bis)urea and (bis)thiourea LSD1 inhibitors that increase cellular levels of H3K4me and H3K4me2, promote the re-expression of silenced tumor suppressor genes and suppress tumor growth in vitro. Here we report the design additional (bis)urea and (bis)thiourea LSD1 inhibitors that feature 3-5-3 or 3-6-3 carbon backbone architectures. Three of these compounds displayed single-digit IC50 values in a recombinant LSD1 assay. In addition, compound 6d exhibited an IC50 of 4.2 μM against the Calu-6 human lung adenocarcinoma line, and 4.8 μM against the MCF7 breast tumor cell line, in an MTS cell viability assay. Following treatment with 6b–6d, Calu-6 cells exhibited a significant increase in the mRNA expression for the silenced tumor suppressor genes SFRP2, HCAD and p16, and modest increases in GATA4 message. The compounds described in this paper represent the most potent epigenetic modulators in this series, and have potential for use as antitumor agents.

Targeting polyamine metabolism for cancer therapy and prevention

“…Therefore, the polyamine analogs provided the first proof of principle that LSD1 could be targeted as an anticancer strategy both in vitro and in vivo [102,103]. Efforts continue to improve upon this paradigm with the goal of designing more selective and potent inhibitors of LSD1 that have the added benefit of being targeting to chromatin [104–107]. Although the polyamine analogs targeting LSD1 were first into this new pharmacologic space for cancer therapy, none have yet made it into the clinical trial.…”

Antibacterial Diamines Targeting Bacterial Membranes

“…The (bis)ureido- and (bis)thioureido diamines 1 – 12 described in this article were synthesized according to our recently published pathway, 18 as shown in Scheme 1. The synthesis of compound 3 is described below, and all other compounds were synthesized in exactly the same manner.…”

LSD1 Histone Demethylase Assays and Inhibition

“…Other compounds beyond tranylcypromine and phenelzine analogs have been reported as LSD1 inhibitors including polyamines (Nowotarski et al, 2015) and hydrazone HCI-2509 but whose specificity and mechanisms of inhibition remain less well characterized (Wang, Huang, et al, 2015). Given that many of the in vitro LSD1 demethylase assays employ peroxidase as an indirect measure of LSD1 enzymatic activity, and the peroxidase activity can be interfered with by particular compounds, it is critical to use secondary assays such as mass spectrometry analysis that directly monitors peptide methylation status to ensure the reliability of a particular LSD1 inhibitor finding.…”