Protein Recognition by Short Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase

Abstract

The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcription factors of the SNAIL1 family, which therefore can competitively inhibit the binding of the N-terminal tail of the histone substrate. Our enzymatic, crystallographic, spectroscopic, and computational studies reveal that LSD1/CoREST can bind to a hexapeptide derived from the SNAIL sequence through recognition of a positively charged α-helical turn that forms upon binding to the enzyme. Variations in sequence and length of this six amino acid ligand modulate affinities enabling the same binding site to differentially interact with proteins that exert distinct biological functions. The discovered short peptide inhibitors exhibit antiproliferative activities and lay the foundation for the development of peptidomimetic small molecule inhibitors of LSD1.

Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin

“…This peptide was investigated in the framework of a study aimed at identifying the sequence features that confer specificity to the interaction between the LSD1/CoREST active site and the N-terminal SNAG domain of SNAIL1 and related transcription factors [16], [49]. Interestingly, the crystallographic analysis revealed that this peptide binds not only to the catalytic site but also in a distinct shallow cleft in the AOD domain (Figure 6).…”

“…The crystallographic data and three-dimensional structure of LSD1/CoREST bound to the peptide Pro-Leu-Ser-Phe-Leu-Val were described before [16] (PDB ID: 3ZMV). Briefly, the peptide complex was obtained by crystal soaking in solutions consisting of 1.6 M sodium/potassium tartrate, 100 mM N-(2-acetamido)-2-iminodiacetic acid pH 6.5, 10% (v/v) glycerol, and 2–5 mM peptide for 3 h. X-ray diffraction data were collected at 100 K at the Swiss Light Source (Villigen, Switzerland).…”

“…A few LSD1 inhibitors have been reported [6] but they display modest activity, have non-ideal medicinal chemistry features due to their polycationic nature [11], [12] or are poorly selective covalent inhibitors that bind to FAD in the H3-histone N-terminal tail-binding pocket (Figure 1) [13]–[15]. Alternatively, short peptide sequences have been recently designed to bind with affinities comparable to those displayed by the natural H3-histone substrate [16] and are inspiring the development of lead compounds. Recently, our group proposed that druggable regions beyond the AOD active site (Figure 1) might hold the key to developing pharmacologically relevant inhibitors by an allosteric mechanism revealed by extended molecular dynamics (MD) simulations [17], [18].…”

Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts

“…Similarly, (bis)amidines such as CBB1007 [51] have been reported as reversible LSD1 inhibitors to selectively target cancer stem cells derepressing epigenetically suppressed genes in vivo. Also peptides were described as LSD1 inhibitors, such as the pLys4Met peptide [52], some synthetic cyclic peptides [53], and a series of short peptides based on the SNAIL sequence exhibiting antiproliferative activities [54]. Among reversible LSD1 inhibitors, amidoximes 7 [55], dithiocarbamates 8 [56], substituted triazoles 9 [57], and benzohydrazides 10 [58] have been recently reported.…”

Analysis of the levels of lysine-specific demethylase 1 (LSD1) mRNA in human ovarian tumors and the effects of chemical LSD1 inhibitors in ovarian cancer cell lines

“…The LSD1 inhibitory activity of pargyline has been tested in prostate cancer cells [7]. Finally, a fourth class of LSD1 inhibitors mimics the peptide structure of LSD1 substrates, such as histone H3 tails [35,36]. For example, CBB1007 is an amidino-guanidinium compound that was developed based on the crystal structure of LSD1 associated with a peptide inhibitor derived from the N-terminal tail of H3 [36].…”