Unveiling New Binding Sites and Allosteric Regulation Mechanisms of LSD1 for Novel Therapeutics

Lysine-specific demethylase 1 (LSD1) regulates key cellular processes through both demethylase-dependent and -independent functions. Current clinical LSD1 inhibitors target its demethylase functions, and issues like the inability to fully modulate LSD1’s demethylase-independent functions have limited their clinical efficacy. SP2509, an allosteric LSD1 inhibitor, can affect both demethylase-dependent and -independent functions of LSD1. Understanding the allosteric regulation mechanisms of SP2509 may facilitate the development of new LSD1 inhibitors. Using SP2509 as a probe, two new binding modes are identified in this work, both of which can alter the conformation of substrate binding pocket, effectively blocking H3 substrate binding and inhibiting the demethylase activity. Interestingly, one binding mode induces significant allosteric bending of Tower/CoREST domain, disrupting the nucleosome substrate binding─an effect not previously reported. This unique binding mode is also validated through in vitro biochemical characterizations. These findings provide invaluable structural insights for designing next-generation LSD1 inhibitors for novel therapeutics.