Amino-carboxamide benzothiazoles as potential LSD1 hit inhibitors. Part I: Computational fragment-based drug design

Abstract

The lysine specific demethylase enzyme LSD1 regulates the function of histone proteins in cells through the demethylation of specific lysine amino acid residues. Being overexpressed in various cancers, LSD1 is considered as a validated target for cancer treatment. In this study, we describe the discovery of novel LSD1 inhibitors using computational fragment-based drug design approach. Structure-based screening of the Maybridge Ro3 2000 Diversity Fragment Library had identified two sets of fragments that bind to two different regions within the LSD1 active site. De Novo and Multiple Copy Simultaneous search (MCSS) docking, ligand efficiency (LE), and binding energy calculations (BE) had assisted the selection of the best scoring fragments that were grown to produce lead-like compounds. The final grown compounds were docked into the active site of the enzyme using flexible docking and their total binding energies were calculated in order to aid the selection of potential LSD1 inhibitors that will be synthesized and biologically evaluated. Six compounds were synthesized and biologically tested, of which two had showed a promising activity against LSD1. Compound 37, with an amino-carboxamide benzothiazole scaffold, showed the best inhibitory activity with an IC50 value of 18.4 μM. Compound 37 was chosen as an LSD1 hit inhibitor worthy of further optimization.